Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Abstract

Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as wellmore » as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7];  [1];  [8];  [4];  [2];  [6];  [5];  [9];  [1]
+ Show Author Affiliations
  1. Univ. of Kansas, Lawrence, KS (United States). Dept. of Molecular Biosciences and Center for Computational Biology
  2. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
  3. Korean Inst. of Science and Technology Information, Daejeon (Korea)
  4. Stanford Univ., CA (United States). Dept. of Bioengineering
  5. Univ. of Maryland, College Park, MD (United States). Dept. of Pharmaceutical Sciences
  6. Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemistry
  7. Harvard Medical School, Boston, MA (United States). Cancer Research Inst.
  8. Argonne National Lab. (ANL), Argonne, IL (United States)
  9. Univ. of Maryland, College Park, MD (United States). Dept. of Chemical and Biomolecular Engineering
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1261132
Grant/Contract Number:  
DBI-1145652; DBI-1145987; MCB-1149187; MCB-1157677; F32GM109632; GM037554; GM051501; GM070855; GM103695; R01GM072558; U54GM087519; KSC-2015-C3-004
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., and Im, Wonpil. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. United States: N. p., 2015. Web. doi:10.1021/acs.jctc.5b00935.
Copy to clipboard
Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., & Im, Wonpil. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. United States. https://doi.org/10.1021/acs.jctc.5b00935
Copy to clipboard
Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., and Im, Wonpil. Thu . "CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field". United States. https://doi.org/10.1021/acs.jctc.5b00935. https://www.osti.gov/servlets/purl/1261132.
Copy to clipboard
@article{osti_1261132,
title = {CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field},
author = {Lee, Jumin and Cheng, Xi and Swails, Jason M. and Yeom, Min Sun and Eastman, Peter K. and Lemkul, Justin A. and Wei, Shuai and Buckner, Joshua and Jeong, Jong Cheol and Qi, Yifei and Jo, Sunhwan and Pande, Vijay S. and Case, David A. and Brooks, Charles L. and MacKerell, Alexander D. and Klauda, Jeffery B. and Im, Wonpil},
abstractNote = {Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.},
doi = {10.1021/acs.jctc.5b00935},
journal = {Journal of Chemical Theory and Computation},
number = 1,
volume = 12,
place = {United States},
year = {Thu Nov 12 00:00:00 EST 2015},
month = {Thu Nov 12 00:00:00 EST 2015}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acs.jctc.5b00935
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 1339 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Cholesterol, sphingolipids, and glycolipids: What do we know about their role in raft-like membranes?
journal, December 2014

The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers
journal, January 2014

  • Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus
  • Journal of the American Chemical Society, Vol. 136, Issue 2
  • DOI: 10.1021/ja4105667

Lipid Organization of the Plasma Membrane
journal, October 2014

  • Ingólfsson, Helgi I.; Melo, Manuel N.; van Eerden, Floris J.
  • Journal of the American Chemical Society, Vol. 136, Issue 41
  • DOI: 10.1021/ja507832e

Membrane lipids: where they are and how they behave
journal, February 2008

  • van Meer, Gerrit; Voelker, Dennis R.; Feigenson, Gerald W.
  • Nature Reviews Molecular Cell Biology, Vol. 9, Issue 2
  • DOI: 10.1038/nrm2330

Probing the importance of lipid diversity in cell membranes via molecular simulation
journal, November 2015

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
journal, August 2015

  • Qi, Yifei; Ingólfsson, Helgi I.; Cheng, Xi
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 9
  • DOI: 10.1021/acs.jctc.5b00513

Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
journal, January 2011

  • Lim, Joseph B.; Klauda, Jeffery B.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1808, Issue 1
  • DOI: 10.1016/j.bbamem.2010.07.036

Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain
journal, May 2012

  • Pandit, Kunal R.; Klauda, Jeffery B.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 5
  • DOI: 10.1016/j.bbamem.2012.01.009

E. coli Outer Membrane and Interactions with OmpLA
journal, June 2014

  • Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun
  • Biophysical Journal, Vol. 106, Issue 11
  • DOI: 10.1016/j.bpj.2014.04.024

ST-analyzer: A web-based user interface for simulation trajectory analysis
journal, March 2014

  • Jeong, Jong Cheol; Jo, Sunhwan; Wu, Emilia L.
  • Journal of Computational Chemistry, Vol. 35, Issue 12
  • DOI: 10.1002/jcc.23584

Molecular Simulation Approaches to Membrane Proteins
journal, November 2011

Computational characterization of structural dynamics underlying function in active membrane transporters
journal, April 2015

Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations
journal, November 2012

Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation
journal, December 2010

  • Pendse, Pushkar Y.; Brooks, Bernard R.; Klauda, Jeffery B.
  • Journal of Molecular Biology, Vol. 404, Issue 3
  • DOI: 10.1016/j.jmb.2010.09.045

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
journal, November 2015

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

  • Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
  • The Journal of Physical Chemistry B, Vol. 114, Issue 23
  • DOI: 10.1021/jp101759q

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature
journal, July 2014

  • Venable, Richard M.; Sodt, Alexander J.; Rogaski, Brent
  • Biophysical Journal, Vol. 107, Issue 1
  • DOI: 10.1016/j.bpj.2014.05.034

Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms
journal, April 2014

  • Wu, Emilia L.; Qi, Yifei; Song, Kevin C.
  • The Journal of Physical Chemistry B, Vol. 118, Issue 16
  • DOI: 10.1021/jp500610t

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
journal, August 2014

  • Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan
  • Journal of Computational Chemistry, Vol. 35, Issue 27
  • DOI: 10.1002/jcc.23702

Influence of Ester-Modified Lipids on Bilayer Structure
journal, November 2013

  • Villanueva, Diana Y.; Lim, Joseph B.; Klauda, Jeffery B.
  • Langmuir, Vol. 29, Issue 46
  • DOI: 10.1021/la403919h

Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
journal, July 2012

  • Klauda, Jeffery B.; Monje, Viviana; Kim, Taehoon
  • The Journal of Physical Chemistry B, Vol. 116, Issue 31
  • DOI: 10.1021/jp304056p

Update of the Cholesterol Force Field Parameters in CHARMM
journal, December 2011

  • Lim, Joseph B.; Rogaski, Brent; Klauda, Jeffery B.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 1
  • DOI: 10.1021/jp207925m

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
journal, September 2013

Lipid14: The Amber Lipid Force Field
journal, January 2014

  • Dickson, Callum J.; Madej, Benjamin D.; Skjevik, Åge A.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 2
  • DOI: 10.1021/ct4010307

An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes
journal, July 2012

  • Jämbeck, Joakim P. M.; Lyubartsev, Alexander P.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 8
  • DOI: 10.1021/ct300342n

Another Piece of the Membrane Puzzle: Extending Slipids Further
journal, October 2012

  • Jämbeck, Joakim P. M.; Lyubartsev, Alexander P.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300777p

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids
journal, March 2012

  • Jämbeck, Joakim P. M.; Lyubartsev, Alexander P.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 10
  • DOI: 10.1021/jp212503e

CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

New spherical-cutoff methods for long-range forces in macromolecular simulation
journal, July 1994

  • Steinbach, Peter J.; Brooks, Bernard R.
  • Journal of Computational Chemistry, Vol. 15, Issue 7
  • DOI: 10.1002/jcc.540150702

A smooth particle mesh Ewald method
journal, November 1995

  • Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
  • The Journal of Chemical Physics, Vol. 103, Issue 19
  • DOI: 10.1063/1.470117

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
journal, November 2012

  • Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300857j

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
journal, April 2011

  • Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart
  • Journal of Computational Chemistry, Vol. 32, Issue 9
  • DOI: 10.1002/jcc.21777

Additive empirical force field for hexopyranose monosaccharides
journal, November 2008

  • Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh
  • Journal of Computational Chemistry, Vol. 29, Issue 15
  • DOI: 10.1002/jcc.21004

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
journal, January 2009

  • Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.
  • Journal of Computational Chemistry
  • DOI: 10.1002/jcc.21367

Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
journal, September 2007

CHARMM-GUI: A web-based graphical user interface for CHARMM
journal, March 2008

  • Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G.
  • Journal of Computational Chemistry, Vol. 29, Issue 11
  • DOI: 10.1002/jcc.20945

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
journal, July 2009

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Solvent-Induced Forces between Two Hydrophilic Groups
journal, February 1994

  • Durell, Stewart R.; Brooks, Bernard R.; Ben-Naim, Arieh
  • The Journal of Physical Chemistry, Vol. 98, Issue 8
  • DOI: 10.1021/j100059a038

Simulation of activation free energies in molecular systems
journal, August 1996

  • Neria, Eyal; Fischer, Stefan; Karplus, Martin
  • The Journal of Chemical Physics, Vol. 105, Issue 5
  • DOI: 10.1063/1.472061

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977

  • Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
  • Journal of Computational Physics, Vol. 23, Issue 3
  • DOI: 10.1016/0021-9991(77)90098-5

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

Constant pressure molecular dynamics algorithms
journal, September 1994

  • Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
  • The Journal of Chemical Physics, Vol. 101, Issue 5
  • DOI: 10.1063/1.467468

Constant pressure molecular dynamics simulation: The Langevin piston method
journal, September 1995

  • Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W.
  • The Journal of Chemical Physics, Vol. 103, Issue 11
  • DOI: 10.1063/1.470648

A molecular dynamics method for simulations in the canonical ensemble
journal, June 1984

Canonical dynamics: Equilibrium phase-space distributions
journal, March 1985

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

Constant pressure molecular dynamics for molecular systems
journal, December 1983

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling
journal, September 1995

Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
journal, January 2004

Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities
journal, July 1999

  • Feller, Scott E.; Pastor, Richard W.
  • The Journal of Chemical Physics, Vol. 111, Issue 3
  • DOI: 10.1063/1.479313

Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers
journal, April 2012

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data
journal, September 2008

Effect of Chain Length and Unsaturation on Elasticity of Lipid Bilayers
journal, July 2000

Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains
journal, January 2006

  • Kučerka, Norbert; Tristram-Nagle, Stephanie; Nagle, John F.
  • Journal of Membrane Biology, Vol. 208, Issue 3
  • DOI: 10.1007/s00232-005-7006-8

The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations
journal, January 2014

  • Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca
  • Soft Matter, Vol. 10, Issue 21
  • DOI: 10.1039/c4sm00066h

Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations
journal, September 2015

  • Konas, Ryan M.; Daristotle, John L.; Harbor, Ndubuisi B.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 41
  • DOI: 10.1021/acs.jpcb.5b06066

Structure and Lipid Interaction of N-Palmitoylsphingomyelin in Bilayer Membranes as Revealed by 2H-NMR Spectroscopy
journal, February 2006

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

Additive empirical force field for hexopyranose monosaccharides
journal, November 2008

  • Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh
  • Journal of Computational Chemistry, Vol. 29, Issue 15
  • DOI: 10.1002/jcc.21004

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
journal, January 2009

  • Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.
  • Journal of Computational Chemistry
  • DOI: 10.1002/jcc.21367

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
journal, April 2011

  • Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart
  • Journal of Computational Chemistry, Vol. 32, Issue 9
  • DOI: 10.1002/jcc.21777

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
journal, August 2014

  • Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan
  • Journal of Computational Chemistry, Vol. 35, Issue 27
  • DOI: 10.1002/jcc.23702

New spherical-cutoff methods for long-range forces in macromolecular simulation
journal, July 1994

  • Steinbach, Peter J.; Brooks, Bernard R.
  • Journal of Computational Chemistry, Vol. 15, Issue 7
  • DOI: 10.1002/jcc.540150702

Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
journal, January 2011

  • Lim, Joseph B.; Klauda, Jeffery B.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1808, Issue 1
  • DOI: 10.1016/j.bbamem.2010.07.036

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
journal, July 2009

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
journal, September 2013

E. coli Outer Membrane and Interactions with OmpLA
journal, June 2014

  • Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun
  • Biophysical Journal, Vol. 106, Issue 11
  • DOI: 10.1016/j.bpj.2014.04.024

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature
journal, July 2014

  • Venable, Richard M.; Sodt, Alexander J.; Rogaski, Brent
  • Biophysical Journal, Vol. 107, Issue 1
  • DOI: 10.1016/j.bpj.2014.05.034

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
journal, November 2015

Probing the importance of lipid diversity in cell membranes via molecular simulation
journal, November 2015

Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
journal, January 2004

Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation
journal, December 2010

  • Pendse, Pushkar Y.; Brooks, Bernard R.; Klauda, Jeffery B.
  • Journal of Molecular Biology, Vol. 404, Issue 3
  • DOI: 10.1016/j.jmb.2010.09.045

Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations
journal, November 2012

Computational characterization of structural dynamics underlying function in active membrane transporters
journal, April 2015

Mechanism of the Lamellar/Inverse Hexagonal Phase Transition Examined by High Resolution X-Ray Diffraction
journal, May 2003

Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations
journal, September 2015

  • Konas, Ryan M.; Daristotle, John L.; Harbor, Ndubuisi B.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 41
  • DOI: 10.1021/acs.jpcb.5b06066

Another Piece of the Membrane Puzzle: Extending Slipids Further
journal, October 2012

  • Jämbeck, Joakim P. M.; Lyubartsev, Alexander P.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300777p

Lipid14: The Amber Lipid Force Field
journal, January 2014

  • Dickson, Callum J.; Madej, Benjamin D.; Skjevik, Åge A.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 2
  • DOI: 10.1021/ct4010307

The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers
journal, January 2014

  • Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus
  • Journal of the American Chemical Society, Vol. 136, Issue 2
  • DOI: 10.1021/ja4105667

Lipid Organization of the Plasma Membrane
journal, October 2014

  • Ingólfsson, Helgi I.; Melo, Manuel N.; van Eerden, Floris J.
  • Journal of the American Chemical Society, Vol. 136, Issue 41
  • DOI: 10.1021/ja507832e

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids
journal, March 2012

  • Jämbeck, Joakim P. M.; Lyubartsev, Alexander P.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 10
  • DOI: 10.1021/jp212503e

Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
journal, July 2012

  • Klauda, Jeffery B.; Monje, Viviana; Kim, Taehoon
  • The Journal of Physical Chemistry B, Vol. 116, Issue 31
  • DOI: 10.1021/jp304056p

Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms
journal, April 2014

  • Wu, Emilia L.; Qi, Yifei; Song, Kevin C.
  • The Journal of Physical Chemistry B, Vol. 118, Issue 16
  • DOI: 10.1021/jp500610t

Molecular basis for assembly of the shieldin complex and its implications for NHEJ
journal, April 2020

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

Constant pressure molecular dynamics for molecular systems
journal, December 1983

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data
journal, September 2008

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Discovering the chloride pathway in the CFTR channel
    journal, July 2019

    Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
    journal, November 2019

    Perspective on computational simulations of glycosaminoglycans
    journal, July 2018

    • Nagarajan, Balaji; Sankaranarayanan, Nehru Viji; Desai, Umesh R.
    • WIREs Computational Molecular Science, Vol. 9, Issue 2
    • DOI: 10.1002/wcms.1388

    Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA
    posted_content, January 2020

    Structural insights into adiponectin receptors suggest ceramidase activity
    journal, March 2017

    • Vasiliauskaité-Brooks, Ieva; Sounier, Remy; Rochaix, Pascal
    • Nature, Vol. 544, Issue 7648
    • DOI: 10.1038/nature21714

    The ghrelin O -acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation
    journal, August 2019

    • Campaña, Maria B.; Irudayanathan, Flaviyan Jerome; Davis, Tasha R.
    • Journal of Biological Chemistry, Vol. 294, Issue 39
    • DOI: 10.1074/jbc.ac119.009749

    Drug-induced diabetes type 2: In silico study involving class B GPCRs
    journal, January 2019

    Molecular characterization of known and novel ACVR1 variants in phenotypes of aberrant ossification
    journal, June 2019

    • Gupta, Aditi; Zimmermann, Michael T.; Wang, Haitao
    • American Journal of Medical Genetics Part A, Vol. 179, Issue 9
    • DOI: 10.1002/ajmg.a.61274

    Modeling of Ion and Water Transport in the Biological Nanopore ClyA
    posted_content, January 2020

    A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
    journal, September 2017

    Symmetry-breaking transitions in the early steps of protein self-assembly
    journal, March 2020

    • La Rosa, Carmelo; Condorelli, Marcello; Compagnini, Giuseppe
    • European Biophysics Journal, Vol. 49, Issue 2
    • DOI: 10.1007/s00249-020-01424-1

    A new computational method for membrane compressibility: Bilayer mechanical thickness revisited
    journal, October 2018

    • Doktorova, M.; LeVine, M. V.; Khelashvili, G.
    • Biophysical Journal
    • DOI: 10.1101/360792

    Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits
    journal, October 2018

    • Na, Sehee; Steinbrecher, Thomas; Koslowski, Thorsten
    • Journal of Computational Chemistry, Vol. 39, Issue 30
    • DOI: 10.1002/jcc.25615

    The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor
    journal, July 2019

    • LeVine, Michael V.; Terry, Daniel S.; Khelashvili, George
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 32
    • DOI: 10.1073/pnas.1903020116

    Augmenting the antinociceptive effects of nicotinic acetylcholine receptor activity through lynx1 modulation
    journal, July 2018

    Cell‐permeable high‐affinity tracers for G q proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors
    journal, February 2020

    • Kuschak, Markus; Namasivayam, Vigneshwaran; Rafehi, Muhammad
    • British Journal of Pharmacology, Vol. 177, Issue 8
    • DOI: 10.1111/bph.14960

    Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity
    journal, February 2019

    Structural insight into YcbB-mediated beta-lactam resistance in Escherichia coli
    journal, April 2019

    • Caveney, Nathanael A.; Caballero, Guillermo; Voedts, Henri
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-09507-0

    Local accumulation of diacylglycerol alters membrane properties nonlinearly due to its transbilayer activity
    journal, June 2019

    Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation
    journal, May 2018

    • Viennet, Thibault; Wördehoff, Michael M.; Uluca, Boran
    • Communications Biology, Vol. 1, Issue 1
    • DOI: 10.1038/s42003-018-0049-z

    Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria
    journal, October 2019

    Congenital myopathy‐related mutations in tropomyosin disrupt regulatory function through altered actin affinity and tropomodulin binding
    journal, March 2019

    • Moraczewska, Joanna; Robaszkiewicz, Katarzyna; Śliwinska, Małgorzata
    • The FEBS Journal, Vol. 286, Issue 10
    • DOI: 10.1111/febs.14787

    Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens
    journal, July 2016

    • Khan, Faez Iqbal; Nizami, Bilal; Anwer, Razique
    • Journal of Biomolecular Structure and Dynamics, Vol. 35, Issue 10
    • DOI: 10.1080/07391102.2016.1206837

    Cooperative Non-bonded Forces Control Membrane Binding of the pH-Low Insertion Peptide pHLIP
    posted_content, June 2018

    • Gupta, C.; Ren, Y.; Mertz, B.
    • Biophysical Journal
    • DOI: 10.1101/341628

    Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy
    journal, December 2018

    • Vasiliauskaité-Brooks, Ieva; Healey, Robert D.; Rochaix, Pascal
    • Nature Communications, Vol. 9, Issue 1
    • DOI: 10.1038/s41467-018-07864-w

    Salvianolic acids from antithrombotic Traditional Chinese Medicine Danshen are antagonists of human P2Y1 and P2Y12 receptors
    journal, May 2018

    CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
    journal, February 2019

    Characterization of the Pseudomonas aeruginosa NQR complex, a bacterial proton pump with roles in autopoisoning resistance
    journal, August 2018

    • Raba, Daniel A.; Rosas-Lemus, Monica; Menzer, William M.
    • Journal of Biological Chemistry, Vol. 293, Issue 40
    • DOI: 10.1074/jbc.ra118.003194

    Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity
    journal, May 2019

    • Sotudeh, Noori; Morales, Paula; Hurst, Dow P.
    • International Journal of Molecular Sciences, Vol. 20, Issue 9
    • DOI: 10.3390/ijms20092300

    Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields
    journal, January 2020

    Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applications
    journal, January 2018

    • Gilmore, Sean F.; Carpenter, Timothy S.; Ingólfsson, Helgi I.
    • Nanoscale, Vol. 10, Issue 16
    • DOI: 10.1039/c7nr09690a

    OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
    journal, July 2017

    Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments
    journal, September 2018

    • Preciado, Lina; Pereañez, Jaime; Azhagiya Singam, Ettayapuram
    • Toxins, Vol. 10, Issue 10
    • DOI: 10.3390/toxins10100397

    Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP
    journal, March 2019

    Novel analogs of sulfasalazine as system x c − antiporter inhibitors: Insights from the molecular modeling studies
    journal, June 2019

    • Patel, Dhavalkumar; Kharkar, Prashant S.; Gandhi, Neha S.
    • Drug Development Research, Vol. 80, Issue 6
    • DOI: 10.1002/ddr.21557

    Computer aided protein engineering to enhance the thermo-stability of CXCR1- T4 lysozyme complex
    journal, March 2019

    Soluble klotho regulates TRPC6 calcium signaling via lipid rafts, independent of the FGFR‐FGF23 pathway
    journal, May 2019

    • Wright, Jon D.; An, Sung‐Wan; Xie, Jian
    • The FASEB Journal, Vol. 33, Issue 8
    • DOI: 10.1096/fj.201900321r

    Polarizable force field for RNA based on the classical drude oscillator: Polarizable Force Field for RNA Based on the Classical Drude Oscillator
    journal, December 2018

    • Lemkul, Justin A.; MacKerell, Alexander D.
    • Journal of Computational Chemistry, Vol. 39, Issue 32
    • DOI: 10.1002/jcc.25709

    Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation
    journal, April 2018

    • Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji
    • The Journal of Chemical Physics, Vol. 148, Issue 16
    • DOI: 10.1063/1.5008438

    Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods
    journal, September 2016

    Selectivity filter modalities and rapid inactivation of the hERG1 channel
    journal, January 2020

    • Miranda, Williams E.; DeMarco, Kevin R.; Guo, Jiqing
    • Proceedings of the National Academy of Sciences, Vol. 117, Issue 6
    • DOI: 10.1073/pnas.1909196117

    Xanthine oxidase inhibitory activity of new pyrrole carboxamide derivatives: In vitro and in silico studies
    journal, August 2018

    • Kıbrız, İbrahim Evren; Saçmacı, Mustafa; Yıldırım, İsmail
    • Archiv der Pharmazie, Vol. 351, Issue 10
    • DOI: 10.1002/ardp.201800165

    Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
    journal, November 2019

    • Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias
    • Journal of Biomolecular NMR, Vol. 74, Issue 1
    • DOI: 10.1007/s10858-019-00289-7

    Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs
    journal, November 2019

    Sequential activation of STIM1 links Ca 2+ with luminal domain unfolding
    journal, November 2019

    β11-12 linker isomerization governs acid-sensing ion channel desensitization and recovery
    journal, February 2020

    Cholesterol suppresses membrane leakage by decreasing water penetrability
    journal, January 2018

    • Bu, Bing; Crowe, Michael; Diao, Jiajie
    • Soft Matter, Vol. 14, Issue 25
    • DOI: 10.1039/c8sm00644j

    Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane
    journal, February 2018

    • Hung, Huynh Minh; Hang, Tran Dieu; Nguyen, Minh Tho
    • Proteins: Structure, Function, and Bioinformatics, Vol. 86, Issue 4
    • DOI: 10.1002/prot.25458

    Brettanomyces bruxellensis SSU1 Haplotypes Confer Different Levels of Sulfite Tolerance When Expressed in a Saccharomyces cerevisiae SSU1 Null Mutant
    journal, December 2018

    • Varela, C.; Bartel, C.; Roach, M.
    • Applied and Environmental Microbiology, Vol. 85, Issue 4
    • DOI: 10.1128/aem.02429-18

    Chemical‐Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors
    journal, April 2020

    • Creutznacher, Robert; Schulze, Eric; Wallmann, Georg
    • ChemBioChem, Vol. 21, Issue 7
    • DOI: 10.1002/cbic.201900572

    L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction
    journal, April 2019

    • Errasti-Murugarren, Ekaitz; Fort, Joana; Bartoccioni, Paola
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-09837-z

    A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition
    journal, January 2018

    The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations
    journal, November 2019

    Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate
    journal, January 2019

    Potential of Matrix Metalloproteinase Inhibitors for the Treatment of Local Tissue Damage Induced by a Type P-I Snake Venom Metalloproteinase
    journal, December 2019

    • Preciado, Lina María; Pereañez, Jaime Andrés; Comer, Jeffrey
    • Toxins, Vol. 12, Issue 1
    • DOI: 10.3390/toxins12010008

    Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10
    journal, November 2019

    Specific Residues in a Purine Transporter Are Critical for Dimerization, ER Exit, and Function
    journal, October 2019

    Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces
    journal, September 2018

    • Osborne, Amy J.; Nan, Ruodan; Miller, Ami
    • Journal of Biological Chemistry, Vol. 293, Issue 44
    • DOI: 10.1074/jbc.ra118.004767

    New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
    text, January 2017

    Molecular dynamics simulation and binding free energy calculations of microcin J25 binding to the FhuA receptor
    journal, April 2020

    Anomalous behavior of membrane fluidity caused by copper-copper bond coupled phospholipids
    journal, September 2018

    Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation
    journal, May 2019

    Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death
    journal, May 2019

    Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models
    journal, January 2018

    The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1
    posted_content, January 2018

    • Hofbauer, Harald F.; Gecht, Michael; Fischer, Sabine C.
    • Journal of Cell Biology
    • DOI: 10.1101/250019

    Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components
    journal, July 2017

    Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities
    journal, July 2019

    Determination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation
    journal, October 2018

    • Bayel Secinti, Burcu; Tatar, Gizem; Taskin Tok, Tugba
    • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 9
    • DOI: 10.1080/07391102.2018.1491420

    Structure of the human ClC-1 chloride channel
    journal, April 2019

    Probing the functional conformations of an atypical proline-rich fusion peptide
    journal, January 2019

    • Dutta, Nivedita; Dutta Chowdhury, Saikat; Lahiri, Ansuman
    • Physical Chemistry Chemical Physics, Vol. 21, Issue 37
    • DOI: 10.1039/c9cp02216c

    Residue-centric modeling and design of saccharide and glycoconjugate structures
    journal, November 2016

    • Labonte, Jason W.; Adolf-Bryfogle, Jared; Schief, William R.
    • Journal of Computational Chemistry, Vol. 38, Issue 5
    • DOI: 10.1002/jcc.24679

    Molecular dynamics simulations of dihydro‐β‐erythroidine bound to the human α4β2 nicotinic acetylcholine receptor
    journal, June 2019

    • Yu, Rilei; Tae, Han‐Shen; Xu, Qingliang
    • British Journal of Pharmacology, Vol. 176, Issue 15
    • DOI: 10.1111/bph.14698

    Atomistic insight into lipid translocation by a TMEM16 scramblase
    journal, November 2016

    • Bethel, Neville P.; Grabe, Michael
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 49
    • DOI: 10.1073/pnas.1607574113

    Modelling of Ca 2+ -promoted structural effects in wild type and post-translationally modified Connexin26
    journal, November 2019

    Molecular modelling and simulation studies of the Mycobacterium tuberculosis multidrug efflux pump protein Rv1258c
    journal, November 2018

    pVEC hydrophobic N-terminus is critical for antibacterial activity
    journal, May 2018

    • Alaybeyoglu, Begum; Sariyar Akbulut, Berna; Ozkirimli, Elif
    • Journal of Peptide Science, Vol. 24, Issue 6
    • DOI: 10.1002/psc.3083

    GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
    journal, July 2017

    • Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro
    • Journal of Computational Chemistry, Vol. 38, Issue 25
    • DOI: 10.1002/jcc.24874

    Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations
    journal, November 2017

    • Sharma, Vivek; Jambrina, Pablo G.; Kaukonen, Markus
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 48
    • DOI: 10.1073/pnas.1708628114

    3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes
    journal, December 2018

    • Lopes-Rodrigues, Maximilien; Zanuy, David; Alemán, Carlos
    • Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 15
    • DOI: 10.1080/07391102.2018.1529627

    Fragment Based Molecular Dynamics for Drug Design
    book, April 2018

    Functional and structural analysis of rare SLC2A2 variants associated with Fanconi‐Bickel syndrome and metabolic traits
    journal, April 2019

    • Enogieru, Osatohanmwen J.; Ung, Peter M. U.; Yee, Sook Wah
    • Human Mutation
    • DOI: 10.1002/humu.23758

    CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems : CHARMM-GUI
    journal, January 2019

    • Qi, Yifei; Lee, Jumin; Klauda, Jeffery B.
    • Journal of Computational Chemistry, Vol. 40, Issue 7
    • DOI: 10.1002/jcc.25773

    U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids: U-shaped Caveolin-1 Conformations are Tightly Regulated by Hydrogen Bonds with Lipids
    journal, March 2019

    • Park, Soohyung; Glover, Kerney J.; Im, Wonpil
    • Journal of Computational Chemistry, Vol. 40, Issue 16
    • DOI: 10.1002/jcc.25807

    Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states
    journal, May 2019

    • Zheng, Wenjun; Wen, Han
    • Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 10
    • DOI: 10.1002/prot.25707

    Combining theoretical and experimental data to decipher CFTR 3D structures and functions
    journal, May 2018

    • Hoffmann, Brice; Elbahnsi, Ahmad; Lehn, Pierre
    • Cellular and Molecular Life Sciences, Vol. 75, Issue 20
    • DOI: 10.1007/s00018-018-2835-7

    Molecular dynamics and binding energy analysis of Vatairea guianensis lectin: a new tool for cancer studies
    journal, January 2020

    • Cavada, Benildo Sousa; Osterne, Vinicius Jose Silva; Pinto-Junior, Vanir Reis
    • Journal of Molecular Modeling, Vol. 26, Issue 2
    • DOI: 10.1007/s00894-019-4281-3

    Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist
    journal, March 2017

    • Marmolejo-Valencia, A. F.; Martínez-Mayorga, K.
    • Journal of Computer-Aided Molecular Design, Vol. 31, Issue 5
    • DOI: 10.1007/s10822-017-0016-7

    HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions
    journal, July 2018

    • Hollingsworth, Louis R.; Lemkul, Justin A.; Bevan, David R.
    • Biophysical Journal, Vol. 115, Issue 1
    • DOI: 10.1016/j.bpj.2018.05.022

    Long-Ranged Protein-Glycan Interactions Stabilize Von Willebrand Factor A2 Domain from Mechanical Unfolding
    journal, February 2019

    Structural basis for selectivity and diversity in angiotensin II receptors
    journal, April 2017

    • Zhang, Haitao; Han, Gye Won; Batyuk, Alexander
    • Nature, Vol. 544, Issue 7650
    • DOI: 10.1038/nature22035

    Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand
    journal, May 2017

    • Zhang, Xianjun; Zhao, Fei; Wu, Yiran
    • Nature Communications, Vol. 8, Issue 1
    • DOI: 10.1038/ncomms15383

    Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism
    journal, October 2018

    • Nagarathinam, Kumar; Nakada-Nakura, Yoshiko; Parthier, Christoph
    • Nature Communications, Vol. 9, Issue 1
    • DOI: 10.1038/s41467-018-06306-x

    Molecular Mechanism of Resveratrol’s Lipid Membrane Protection
    journal, January 2018

    K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase
    journal, August 2018

    Molecular Dynamics Simulations of the Allosteric Modulation of the Adenosine A2a Receptor by a Mini-G Protein
    journal, April 2019

    Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring
    journal, May 2019

    An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin
    journal, August 2019

    Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog
    journal, November 2019

    Pyrithione-based ruthenium complexes as inhibitors of aldo–keto reductase 1C enzymes and anticancer agents
    journal, January 2016

    • Kljun, Jakob; Anko, Maja; Traven, Katja
    • Dalton Transactions, Vol. 45, Issue 29
    • DOI: 10.1039/c6dt00668j

    Cellulose–hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion
    journal, January 2018

    • Kumar, Rajeev; Bhagia, Samarthya; Smith, Micholas Dean
    • Green Chemistry, Vol. 20, Issue 4
    • DOI: 10.1039/c7gc03518g

    Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles
    journal, January 2020

    • Nademi, Yousef; Tang, Tian; Uludağ, Hasan
    • Nanoscale, Vol. 12, Issue 2
    • DOI: 10.1039/c9nr08128c

    Perspective: Computational modeling of accurate cellular membranes with molecular resolution
    journal, December 2018

    • Klauda, Jeffery B.
    • The Journal of Chemical Physics, Vol. 149, Issue 22
    • DOI: 10.1063/1.5055007

    Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights
    journal, November 2018

    • Hong, Lu; Vani, Bodhi P.; Thiede, Erik H.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 49
    • DOI: 10.1073/pnas.1812555115

    Membrane perforation by the pore-forming toxin pneumolysin
    journal, June 2019

    • Vögele, Martin; Bhaskara, Ramachandra M.; Mulvihill, Estefania
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
    • DOI: 10.1073/pnas.1904304116

    Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells
    journal, July 2017

    • Shindou, Hideo; Koso, Hideto; Sasaki, Junko
    • Journal of Biological Chemistry, Vol. 292, Issue 29
    • DOI: 10.1074/jbc.M117.790568

    Effect of thermostable mutations on the neurotensin receptor 1 (NTSR 1 ) activation state
    journal, February 2019

    • Nagarajan, Shanthi; Alkayed, Nabil J.; Kaul, Sanjiv
    • Journal of Biomolecular Structure and Dynamics, Vol. 38, Issue 2
    • DOI: 10.1080/07391102.2019.1573705

    The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1
    journal, June 2018

    • Hofbauer, Harald F.; Gecht, Michael; Fischer, Sabine C.
    • Journal of Cell Biology, Vol. 217, Issue 9
    • DOI: 10.1083/jcb.201802027

    Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites
    journal, July 2018

    • Wang, Yali; Yang, Elaine; Wells, Marta M.
    • Journal of General Physiology, Vol. 150, Issue 9
    • DOI: 10.1085/jgp.201811993

    Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
    journal, April 2019

    • Balaceanu, Alexandra; Buitrago, Diana; Walther, Jürgen
    • Nucleic Acids Research, Vol. 47, Issue 9
    • DOI: 10.1093/nar/gkz255

    Modulating hinge flexibility in the APP transmembrane domain alters γ-secretase cleavage
    posted_content, November 2018

    • Götz, Alexander; Mylonas, Nadine; Högel, Philipp
    • Biophysical Journal
    • DOI: 10.1101/375006

    Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations
    posted_content, February 2019

    • Wilson, Blake A.; Ramanathan, Arvind; Lopez, Carlos F.
    • Biophysical Journal
    • DOI: 10.1101/557744

    An unusual amino acid substitution within hummingbird cytochrome c oxidase alters a key proton-conducting channel
    posted_content, May 2020

    • Dunn, Cory D.; Akpınar, Bala Anı; Sharma, Vivek
    • G3: Genes|Genomes|Genetics
    • DOI: 10.1101/610915

    Membrane remodeling by the lytic fragment of sticholysin II: implications for the toroidal pore model
    posted_content, April 2019

    • Mesa-Galloso, H.; Valiente, P. A.; Epand, R. F.
    • Biophysical Journal
    • DOI: 10.1101/620336

    The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
    posted_content, September 2019

    • Harkey, Thomas; Kumar, Vivek Govind; Hettige, Jeevapani
    • Scientific Reports
    • DOI: 10.1101/707778

    Systematic cysteine-crosslinking in native membranes establishes the transmembrane architecture in Ire1 clusters
    posted_content, April 2021

    • Väth, Kristina; Covino, Roberto; Reinhard, John
    • Journal of Cell Biology
    • DOI: 10.1101/772772

    Oestrogenic activity of mimosine on MCF-7 breast cancer cell line through the ERα-mediated pathway
    journal, October 2018

    • Huq, AKM Moyeenul; Wai, Lam Kok; Rullah, Kamal
    • Chemical Biology & Drug Design, Vol. 93, Issue 3
    • DOI: 10.1111/cbdd.13404

    ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domain
    journal, November 2018

    • Bulla, M.; Gyimesi, G.; Kim, J. H.
    • The Journal of Physiology, Vol. 597, Issue 2
    • DOI: 10.1113/jp277079

    A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif
    journal, October 2018

    • Utesch, Tillmann; de Miguel Catalina, Alejandra; Schattenberg, Caspar
    • mSphere, Vol. 3, Issue 5
    • DOI: 10.1128/msphere.00377-18

    Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
    journal, May 2019

    Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II
    text, January 2019

    Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin
    journal, December 2019

    • Zhang, Wenying; Yang, Ting; Zhou, Shuangyan
    • Biomolecules, Vol. 9, Issue 12
    • DOI: 10.3390/biom9120852

    Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations
    journal, August 2019

    • Yang, Ting; Zhang, Wenying; Cheng, Jie
    • International Journal of Molecular Sciences, Vol. 20, Issue 15
    • DOI: 10.3390/ijms20153780

    Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin
    journal, October 2018

    Identification and Characterization of NTB451 as a Potential Inhibitor of Necroptosis
    journal, November 2018

    Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones
    journal, February 2020

    Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
    text, January 2020

    • Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias
    • Springer
    • DOI: 10.5167/uzh-177033

    Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations
    text, January 2019

    Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors
    text, January 2019

    Structural insight into the activation of a class B G-protein-coupled receptor by peptide hormones in live human cells
    journal, August 2017

    Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
    journal, July 2020

    • Bengtsen, Tone; Holm, Viktor L.; Kjølbye, Lisbeth Ravnkilde
    • eLife, Vol. 9
    • DOI: 10.7554/eLife.56518

    CHARMM-GUI 10 years for biomolecular modeling and simulation: Biomolecular Modeling and Simulation
    journal, November 2016

    • Jo, Sunhwan; Cheng, Xi; Lee, Jumin
    • Journal of Computational Chemistry, Vol. 38, Issue 15
    • DOI: 10.1002/jcc.24660

    Novel FSHR variants causing female resistant ovary syndrome
    journal, December 2019

    • Khor, Shuzin; Lyu, Qifeng; Kuang, Yanping
    • Molecular Genetics & Genomic Medicine, Vol. 8, Issue 2
    • DOI: 10.1002/mgg3.1082

    Investigating Dual Ca2+ Modulation of the Ryanodine Receptor 1 by Molecular Dynamics Simulation
    journal, February 2020

    Predictive compound accumulation rules yield a broad-spectrum antibiotic
    journal, May 2017

    • Richter, Michelle F.; Drown, Bryon S.; Riley, Andrew P.
    • Nature, Vol. 545, Issue 7654
    • DOI: 10.1038/nature22308

    Hydrophobic gating in BK channels
    journal, August 2018

    An inner activation gate controls TMEM16F phospholipid scrambling
    journal, April 2019

    Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding
    journal, October 2018

    The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
    journal, October 2019

    New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
    journal, February 2017

    • Ishchenko, A.; Round, E.; Borshchevskiy, V.
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep41811

    Rapid diffusion of cholesterol along polyunsaturated membranes via deep dives
    journal, January 2019

    • Javanainen, Matti; Martinez-Seara, Hector
    • Physical Chemistry Chemical Physics, Vol. 21, Issue 22
    • DOI: 10.1039/c9cp02022e

    Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding
    journal, August 2018

    • Madsen, Jesper J.; Grime, John M. A.; Rossman, Jeremy S.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 37
    • DOI: 10.1073/pnas.1805443115

    Structural modeling of human cardiac sodium channel pore domain
    journal, July 2017

    Identification of two natural compound inhibitors of Leishmania donovani Spermidine Synthase (SpdS) through molecular docking and dynamic studies
    journal, August 2017

    • V. M., Vidhya; Dubey, Vikash Kumar; Ponnuraj, Karthe
    • Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 10
    • DOI: 10.1080/07391102.2017.1366947

    Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity
    posted_content, August 2018

    • Manzo, Giorgia; Ferguson, Philip M.; Gustilo, V. Benjamin
    • Scientific Reports
    • DOI: 10.1101/312215

    β11-12 linker isomerization governs Acid-sensing ion channel desensitization and recovery
    posted_content, August 2019

    • Rook, Matthew; Williamson, Abby; Lueck, John D.
    • eLife
    • DOI: 10.1101/746271

    Structural analysis of phosphorylation‐associated interactions of human MCC with Scribble PDZ domains
    journal, July 2019

    • Caria, Sofia; Stewart, Bryce Z.; Jin, Ruitao
    • The FEBS Journal, Vol. 286, Issue 24
    • DOI: 10.1111/febs.15002

    Targeted fluorescence lifetime probes reveal responsive organelle viscosity and membrane fluidity
    journal, February 2019

    Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
    journal, May 2020

    Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane
    journal, September 2019

    • Chen, Ke; Sheng, Yuebiao; Wang, Jun
    • International Journal of Molecular Sciences, Vol. 20, Issue 19
    • DOI: 10.3390/ijms20194760

    Conformational latitude – activity relationship of KPPR tetrapeptide analogues toward their ability to inhibit binding of vascular endothelial growth factor 165 to neuropilin‐1
    journal, May 2017

    • Fedorczyk, Bartlomiej; Lipiński, Piotr F. J.; Tymecka, Dagmara
    • Journal of Peptide Science, Vol. 23, Issue 6
    • DOI: 10.1002/psc.3009

    Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles
    journal, March 2019

    • Doktorova, Milka; Heberle, Frederick A.; Marquardt, Drew
    • Biophysical Journal, Vol. 116, Issue 5
    • DOI: 10.1016/j.bpj.2019.01.016

    Molecular basis of PIP2-dependent regulation of the Ca2+-activated chloride channel TMEM16A
    journal, August 2019

    Binding site opening by loop C shift and chloride ion-pore interaction in the GABA A receptor model
    journal, January 2017

    • Michałowski, M. A.; Kraszewski, S.; Mozrzymas, J. W.
    • Physical Chemistry Chemical Physics, Vol. 19, Issue 21
    • DOI: 10.1039/c7cp00582b

    Na + coordination at the Na2 site of the Na + /I − symporter
    journal, August 2016

    • Ferrandino, Giuseppe; Nicola, Juan Pablo; Sánchez, Yuly E.
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 37
    • DOI: 10.1073/pnas.1607231113

    Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation
    journal, August 2017

    • Gu, Siyi; Sachleben, Joseph R.; Boughter, Christopher T.
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 35
    • DOI: 10.1073/pnas.1707547114

    Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation
    posted_content, August 2019

    • Zheng, Wenjun; Wen, Han
    • Proteins: Structure, Function, and Bioinformatics
    • DOI: 10.1101/736934

    A two-lane mechanism for selective biological ammonium transport
    journal, November 2019

    • Williamson, Gordon; Tamburrino, Giulia; Mirandela, Gaëtan Dias
    • Access Microbiology
    • DOI: 10.1101/849562

    Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus
    journal, September 2019

    • Ojennus, Deanna Dahlke; Bratt, Nicholas J.; Jones, Kent L.
    • Acta Crystallographica Section F Structural Biology Communications, Vol. 75, Issue 10
    • DOI: 10.1107/s2053230x19011774

    Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations
    journal, February 2020

    Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
    journal, April 2018

    An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel
    journal, July 2020

    • Dunn, Cory D.; Akpınar, Bala Anı; Sharma, Vivek
    • G3 Genes|Genomes|Genetics, Vol. 10, Issue 7
    • DOI: 10.1534/g3.120.401312

    Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors
    text, January 2019

    CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations
    journal, July 2019

    • Qi, Yifei; Lee, Jumin; Cheng, Xi
    • Journal of Computational Chemistry, Vol. 41, Issue 5
    • DOI: 10.1002/jcc.26032

    Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions
    journal, November 2019

    • Pachler, Michael; Kabelka, Ivo; Appavou, Marie-Sousai
    • Biophysical Journal, Vol. 117, Issue 10
    • DOI: 10.1016/j.bpj.2019.10.022

    Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors
    journal, January 2019

    SurA is a “Groove-y” Chaperone That Expands Unfolded Outer Membrane Proteins
    posted_content, August 2020

    • Marx, Dagan C.; Plummer, Ashlee M.; Faustino, Anneliese M.
    • Proceedings of the National Academy of Sciences
    • DOI: 10.1101/2019.12.17.878660

    Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP
    posted_content, August 2018

    • Götz, Alexander; Högel, Philipp; Silber, Mara
    • Scientific Reports
    • DOI: 10.1101/372698

    Correction: A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
    journal, February 2018

    Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
    text, January 2020

    Investigating dual Ca 2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation
    journal, July 2020

    • Zheng, Wenjun; Wen, Han
    • Proteins: Structure, Function, and Bioinformatics, Vol. 88, Issue 11
    • DOI: 10.1002/prot.25971

    A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited
    journal, February 2019

    • Doktorova, Milka; LeVine, Michael V.; Khelashvili, George
    • Biophysical Journal, Vol. 116, Issue 3
    • DOI: 10.1016/j.bpj.2018.12.016

    Water for Sterol: an Unusual Mechanism of Sterol Egress from a StARkin Domain
    journal, February 2020

    A two-lane mechanism for selective biological ammonium transport
    journal, July 2020

    • Williamson, Gordon; Dias Mirandela, Gaetan; Tamburrino, Giulia
    • Access Microbiology, Vol. 2, Issue 7A
    • DOI: 10.1099/acmi.ac2020.po0133

    Discovering the chloride pathway in the CFTR channel
    journal, July 2019

    Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations
    journal, February 2016

    • Wieder, Marcus; Perricone, Ugo; Seidel, Thomas
    • Monatshefte für Chemie - Chemical Monthly, Vol. 147, Issue 3
    • DOI: 10.1007/s00706-016-1674-1

    Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
    journal, November 2019

    • Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias
    • Journal of Biomolecular NMR, Vol. 74, Issue 1
    • DOI: 10.1007/s10858-019-00289-7

    Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
    journal, January 2019

    • Pak, Alexander J.; Dannenhoffer-Lafage, Thomas; Madsen, Jesper J.
    • Journal of Chemical Theory and Computation, Vol. 15, Issue 3
    • DOI: 10.1021/acs.jctc.8b01033

    Substrate-Specific Inhibition Constants for Phospholipase A2 Acting on Unique Phospholipid Substrates in Mixed Micelles and Membranes Using Lipidomics
    journal, January 2019

    • Mouchlis, Varnavas D.; Armando, Aaron; Dennis, Edward A.
    • Journal of Medicinal Chemistry, Vol. 62, Issue 4
    • DOI: 10.1021/acs.jmedchem.8b01568

    Unidirectional Transport Mechanism in an ATP Dependent Exporter
    journal, March 2017

    Molecular Basis of the Glucose Transport Mechanism in Plants
    journal, May 2019

    Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands
    journal, June 2018

    Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand
    journal, May 2017

    • Zhang, Xianjun; Zhao, Fei; Wu, Yiran
    • Nature Communications, Vol. 8, Issue 1
    • DOI: 10.1038/ncomms15383

    An inner activation gate controls TMEM16F phospholipid scrambling
    journal, April 2019

    L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction
    journal, April 2019

    • Errasti-Murugarren, Ekaitz; Fort, Joana; Bartoccioni, Paola
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-09837-z

    Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
    journal, November 2019

    Publisher Correction: Hydrophobic gating in BK channels
    journal, September 2020

    Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring
    journal, May 2019

    Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities
    journal, July 2019

    The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
    journal, October 2019

    Asc-1 Transporter (SLC7A10): Homology Models And Molecular Dynamics Insights Into The First Steps Of The Transport Mechanism
    journal, February 2020

    Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog
    journal, November 2019

    New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
    journal, February 2017

    • Ishchenko, A.; Round, E.; Borshchevskiy, V.
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep41811

    Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach
    journal, January 2017

    • Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E.
    • Chemical Science, Vol. 8, Issue 8
    • DOI: 10.1039/c7sc00980a

    Na + coordination at the Na2 site of the Na + /I − symporter
    journal, August 2016

    • Ferrandino, Giuseppe; Nicola, Juan Pablo; Sánchez, Yuly E.
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 37
    • DOI: 10.1073/pnas.1607231113

    The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor
    journal, July 2019

    • LeVine, Michael V.; Terry, Daniel S.; Khelashvili, George
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 32
    • DOI: 10.1073/pnas.1903020116

    Membrane perforation by the pore-forming toxin pneumolysin
    journal, June 2019

    • Vögele, Martin; Bhaskara, Ramachandra M.; Mulvihill, Estefania
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
    • DOI: 10.1073/pnas.1904304116

    Ensemble-based evaluation for protein structure models
    journal, June 2016

    Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
    journal, April 2019

    • Balaceanu, Alexandra; Buitrago, Diana; Walther, Jürgen
    • Nucleic Acids Research, Vol. 47, Issue 9
    • DOI: 10.1093/nar/gkz255

    Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study
    journal, March 2016

    • Leclerc, Fabrice; Zaccai, Giuseppe; Vergne, Jacques
    • Scientific Reports
    • DOI: 10.1101/045054

    Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter
    journal, December 2016

    • Harrigan, Matthew P.; McKiernan, Keri A.; Shanmugasundaram, Veerabahu
    • Scientific Reports
    • DOI: 10.1101/092155

    Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane
    journal, June 2020

    Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level
    journal, July 2020

    • Liekkinen, Juho; de Santos Moreno, Berta; Paananen, Riku O.
    • Frontiers in Cell and Developmental Biology
    • DOI: 10.1101/2020.07.07.191569

    Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP
    posted_content, August 2018

    • Götz, Alexander; Högel, Philipp; Silber, Mara
    • Scientific Reports
    • DOI: 10.1101/372698

    β11-12 linker isomerization governs Acid-sensing ion channel desensitization and recovery
    posted_content, August 2019

    • Rook, Matthew; Williamson, Abby; Lueck, John D.
    • eLife
    • DOI: 10.1101/746271

    A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif
    journal, October 2018

    • Utesch, Tillmann; de Miguel Catalina, Alejandra; Schattenberg, Caspar
    • mSphere, Vol. 3, Issue 5
    • DOI: 10.1128/msphere.00377-18

    Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
    journal, May 2019

    A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
    journal, September 2017

    Augmenting the antinociceptive effects of nicotinic acetylcholine receptor activity through lynx1 modulation
    journal, July 2018

    Drug-induced diabetes type 2: In silico study involving class B GPCRs
    journal, January 2019

    Effect of pressure profile of shock waves on lipid membrane deformation
    journal, February 2019

    Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor
    journal, February 2018

    • Slater, Paula G.; Gutierrez-Maldonado, Sebastian E.; Gysling, Katia
    • Frontiers in Endocrinology, Vol. 9
    • DOI: 10.3389/fendo.2018.00043

    Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity
    journal, May 2019

    • Sotudeh, Noori; Morales, Paula; Hurst, Dow P.
    • International Journal of Molecular Sciences, Vol. 20, Issue 9
    • DOI: 10.3390/ijms20092300

    Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane
    journal, September 2019

    • Chen, Ke; Sheng, Yuebiao; Wang, Jun
    • International Journal of Molecular Sciences, Vol. 20, Issue 19
    • DOI: 10.3390/ijms20194760

    Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin
    journal, October 2018

    NFBTA: A Potent Cytotoxic Agent against Glioblastoma
    journal, June 2019

    Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments
    journal, September 2018

    • Preciado, Lina; Pereañez, Jaime; Azhagiya Singam, Ettayapuram
    • Toxins, Vol. 10, Issue 10
    • DOI: 10.3390/toxins10100397

    Potential of Matrix Metalloproteinase Inhibitors for the Treatment of Local Tissue Damage Induced by a Type P-I Snake Venom Metalloproteinase
    journal, December 2019

    • Preciado, Lina María; Pereañez, Jaime Andrés; Comer, Jeffrey
    • Toxins, Vol. 12, Issue 1
    • DOI: 10.3390/toxins12010008

    Comparison of Sampling Methods via Robust Free Energy Inference: Application to Calmodulin
    preprint, January 2017

    Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components
    journal, July 2017

    Exchange of water for sterol underlies sterol egress from a StARkin domain
    journal, December 2019

    Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models
    journal, January 2018

    A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters.
    text, January 2017

    • Pujol Gimenez, Jonai; Hediger, Matthias; Gyimesi, Gergely
    • Nature Publishing Group
    • DOI: 10.7892/boris.106119
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: