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

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

doi:10.1021/acs.jctc.5b00935

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

Journal Article · Thu Nov 12 00:00:00 EST 2015 · Journal of Chemical Theory and Computation

DOI:https://doi.org/10.1021/acs.jctc.5b00935· OSTI ID:1261132

Lee, Jumin ^[1]; Cheng, Xi ^[1]; Swails, Jason M. ^[2]; Yeom, Min Sun ^[3]; Eastman, Peter K. ^[4]; Lemkul, Justin A. ^[5]; Wei, Shuai ^[6]; Buckner, Joshua ^[6]; Jeong, Jong Cheol ^[7]; Qi, Yifei ^[1]; Jo, Sunhwan ^[8]; Pande, Vijay S. ^[4]; Case, David A. ^[2]; Brooks, Charles L. ^[6]; MacKerell, Alexander D. ^[5]; Klauda, Jeffery B. ^[9]; Im, Wonpil ^[1]

Univ. of Kansas, Lawrence, KS (United States). Dept. of Molecular Biosciences and Center for Computational Biology
Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
Korean Inst. of Science and Technology Information, Daejeon (Korea)
Stanford Univ., CA (United States). Dept. of Bioengineering
Univ. of Maryland, College Park, MD (United States). Dept. of Pharmaceutical Sciences
Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemistry
Harvard Medical School, Boston, MA (United States). Cancer Research Inst.
Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. of Maryland, College Park, MD (United States). Dept. of Chemical and Biomolecular Engineering

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: DBI-1145652; DBI-1145987; MCB-1149187; MCB-1157677; F32GM109632; GM037554; GM051501; GM070855; GM103695; R01GM072558; U54GM087519; KSC-2015-C3-004

OSTI ID:: 1261132

Journal Information:: Journal of Chemical Theory and Computation, Vol. 12, Issue 1; ISSN 1549-9618

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 1339 works

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References (66)

Cholesterol, sphingolipids, and glycolipids: What do we know about their role in raft-like membranes? Róg, Tomasz; Vattulainen, Ilpo Chemistry and Physics of Lipids, Vol. 184 https://doi.org/10.1016/j.chemphyslip.2014.10.004	journal	December 2014
The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus Journal of the American Chemical Society, Vol. 136, Issue 2 https://doi.org/10.1021/ja4105667	journal	January 2014
Lipid Organization of the Plasma Membrane Ingólfsson, Helgi I.; Melo, Manuel N.; van Eerden, Floris J. Journal of the American Chemical Society, Vol. 136, Issue 41 https://doi.org/10.1021/ja507832e	journal	October 2014
Membrane lipids: where they are and how they behave van Meer, Gerrit; Voelker, Dennis R.; Feigenson, Gerald W. Nature Reviews Molecular Cell Biology, Vol. 9, Issue 2 https://doi.org/10.1038/nrm2330	journal	February 2008
Probing the importance of lipid diversity in cell membranes via molecular simulation Khakbaz, Pouyan; Klauda, Jeffery B. Chemistry and Physics of Lipids, Vol. 192 https://doi.org/10.1016/j.chemphyslip.2015.08.003	journal	November 2015
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field Qi, Yifei; Ingólfsson, Helgi I.; Cheng, Xi Journal of Chemical Theory and Computation, Vol. 11, Issue 9 https://doi.org/10.1021/acs.jctc.5b00513	journal	August 2015
Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study Lim, Joseph B.; Klauda, Jeffery B. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1808, Issue 1 https://doi.org/10.1016/j.bbamem.2010.07.036	journal	January 2011
Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain Pandit, Kunal R.; Klauda, Jeffery B. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 5 https://doi.org/10.1016/j.bbamem.2012.01.009	journal	May 2012
E. coli Outer Membrane and Interactions with OmpLA Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun Biophysical Journal, Vol. 106, Issue 11 https://doi.org/10.1016/j.bpj.2014.04.024	journal	June 2014
ST-analyzer: A web-based user interface for simulation trajectory analysis Jeong, Jong Cheol; Jo, Sunhwan; Wu, Emilia L. Journal of Computational Chemistry, Vol. 35, Issue 12 https://doi.org/10.1002/jcc.23584	journal	March 2014
Molecular Simulation Approaches to Membrane Proteins Stansfeld, Phillip J.; Sansom, Mark S. P. Structure, Vol. 19, Issue 11 https://doi.org/10.1016/j.str.2011.10.002	journal	November 2011
Computational characterization of structural dynamics underlying function in active membrane transporters Li, Jing; Wen, Po-Chao; Moradi, Mahmoud Current Opinion in Structural Biology, Vol. 31 https://doi.org/10.1016/j.sbi.2015.04.001	journal	April 2015
Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations Rogaski, Brent; Klauda, Jeffery B. Journal of Molecular Biology, Vol. 423, Issue 5 https://doi.org/10.1016/j.jmb.2012.08.015	journal	November 2012
Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation Pendse, Pushkar Y.; Brooks, Bernard R.; Klauda, Jeffery B. Journal of Molecular Biology, Vol. 404, Issue 3 https://doi.org/10.1016/j.jmb.2010.09.045	journal	December 2010
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model Qi, Yifei; Cheng, Xi; Lee, Jumin Biophysical Journal, Vol. 109, Issue 10 https://doi.org/10.1016/j.bpj.2015.10.008	journal	November 2015
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo The Journal of Physical Chemistry B, Vol. 114, Issue 23 https://doi.org/10.1021/jp101759q	journal	June 2010
CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature Venable, Richard M.; Sodt, Alexander J.; Rogaski, Brent Biophysical Journal, Vol. 107, Issue 1 https://doi.org/10.1016/j.bpj.2014.05.034	journal	July 2014
Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms Wu, Emilia L.; Qi, Yifei; Song, Kevin C. The Journal of Physical Chemistry B, Vol. 118, Issue 16 https://doi.org/10.1021/jp500610t	journal	April 2014
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan Journal of Computational Chemistry, Vol. 35, Issue 27 https://doi.org/10.1002/jcc.23702	journal	August 2014
Influence of Ester-Modified Lipids on Bilayer Structure Villanueva, Diana Y.; Lim, Joseph B.; Klauda, Jeffery B. Langmuir, Vol. 29, Issue 46 https://doi.org/10.1021/la403919h	journal	November 2013
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains Klauda, Jeffery B.; Monje, Viviana; Kim, Taehoon The Journal of Physical Chemistry B, Vol. 116, Issue 31 https://doi.org/10.1021/jp304056p	journal	July 2012
Update of the Cholesterol Force Field Parameters in CHARMM Lim, Joseph B.; Rogaski, Brent; Klauda, Jeffery B. The Journal of Physical Chemistry B, Vol. 116, Issue 1 https://doi.org/10.1021/jp207925m	journal	December 2011
Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics Wu, Emilia L.; Engström, Olof; Jo, Sunhwan Biophysical Journal, Vol. 105, Issue 6 https://doi.org/10.1016/j.bpj.2013.08.002	journal	September 2013
Lipid14: The Amber Lipid Force Field Dickson, Callum J.; Madej, Benjamin D.; Skjevik, Åge A. Journal of Chemical Theory and Computation, Vol. 10, Issue 2 https://doi.org/10.1021/ct4010307	journal	January 2014
An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes Jämbeck, Joakim P. M.; Lyubartsev, Alexander P. Journal of Chemical Theory and Computation, Vol. 8, Issue 8 https://doi.org/10.1021/ct300342n	journal	July 2012
Another Piece of the Membrane Puzzle: Extending Slipids Further Jämbeck, Joakim P. M.; Lyubartsev, Alexander P. Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct300777p	journal	October 2012
Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids Jämbeck, Joakim P. M.; Lyubartsev, Alexander P. The Journal of Physical Chemistry B, Vol. 116, Issue 10 https://doi.org/10.1021/jp212503e	journal	March 2012
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
New spherical-cutoff methods for long-range forces in macromolecular simulation Steinbach, Peter J.; Brooks, Bernard R. Journal of Computational Chemistry, Vol. 15, Issue 7 https://doi.org/10.1002/jcc.540150702	journal	July 1994
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation Eastman, Peter; Friedrichs, Mark S.; Chodera, John D. Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct300857j	journal	November 2012
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 Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart Journal of Computational Chemistry, Vol. 32, Issue 9 https://doi.org/10.1002/jcc.21777	journal	April 2011
Additive empirical force field for hexopyranose monosaccharides Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh Journal of Computational Chemistry, Vol. 29, Issue 15 https://doi.org/10.1002/jcc.21004	journal	November 2008
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields Vanommeslaeghe, K.; Hatcher, E.; Acharya, C. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21367	journal	January 2009
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations Jo, Sunhwan; Kim, Taehoon; Im, Wonpil PLoS ONE, Vol. 2, Issue 9 https://doi.org/10.1371/journal.pone.0000880	journal	September 2007
CHARMM-GUI: A web-based graphical user interface for CHARMM Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G. Journal of Computational Chemistry, Vol. 29, Issue 11 https://doi.org/10.1002/jcc.20945	journal	March 2008
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes Jo, Sunhwan; Lim, Joseph B.; Klauda, Jeffery B. Biophysical Journal, Vol. 97, Issue 1 https://doi.org/10.1016/j.bpj.2009.04.013	journal	July 2009
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Solvent-Induced Forces between Two Hydrophilic Groups Durell, Stewart R.; Brooks, Bernard R.; Ben-Naim, Arieh The Journal of Physical Chemistry, Vol. 98, Issue 8 https://doi.org/10.1021/j100059a038	journal	February 1994
Simulation of activation free energies in molecular systems Neria, Eyal; Fischer, Stefan; Karplus, Martin The Journal of Chemical Physics, Vol. 105, Issue 5 https://doi.org/10.1063/1.472061	journal	August 1996
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L	journal	September 1997
Constant pressure molecular dynamics algorithms Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L. The Journal of Chemical Physics, Vol. 101, Issue 5 https://doi.org/10.1063/1.467468	journal	September 1994
Constant pressure molecular dynamics simulation: The Langevin piston method Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W. The Journal of Chemical Physics, Vol. 103, Issue 11 https://doi.org/10.1063/1.470648	journal	September 1995
A molecular dynamics method for simulations in the canonical ensemble Nosé, Shūichi Molecular Physics, Vol. 52, Issue 2 https://doi.org/10.1080/00268978400101201	journal	June 1984
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
Constant pressure molecular dynamics for molecular systems Nosé, Shuichi; Klein, M. L. Molecular Physics, Vol. 50, Issue 5 https://doi.org/10.1080/00268978300102851	journal	December 1983
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling Chow, Kim-Hung; Ferguson, David M. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00059-O	journal	September 1995
Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm Åqvist, Johan; Wennerström, Petra; Nervall, Martin Chemical Physics Letters, Vol. 384, Issue 4-6 https://doi.org/10.1016/j.cplett.2003.12.039	journal	January 2004
Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities Feller, Scott E.; Pastor, Richard W. The Journal of Chemical Physics, Vol. 111, Issue 3 https://doi.org/10.1063/1.479313	journal	July 1999
Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers Kim, Taehoon; Lee, Kyu Il; Morris, Phillip Biophysical Journal, Vol. 102, Issue 7 https://doi.org/10.1016/j.bpj.2012.03.014	journal	April 2012
Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data Kučerka, Norbert; Nagle, John F.; Sachs, Jonathan N. Biophysical Journal, Vol. 95, Issue 5 https://doi.org/10.1529/biophysj.108.132662	journal	September 2008
Effect of Chain Length and Unsaturation on Elasticity of Lipid Bilayers Rawicz, W.; Olbrich, K. C.; McIntosh, T. Biophysical Journal, Vol. 79, Issue 1 https://doi.org/10.1016/S0006-3495(00)76295-3	journal	July 2000
Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains Kučerka, Norbert; Tristram-Nagle, Stephanie; Nagle, John F. Journal of Membrane Biology, Vol. 208, Issue 3 https://doi.org/10.1007/s00232-005-7006-8	journal	January 2006
The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca Soft Matter, Vol. 10, Issue 21 https://doi.org/10.1039/c4sm00066h	journal	January 2014
Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations Konas, Ryan M.; Daristotle, John L.; Harbor, Ndubuisi B. The Journal of Physical Chemistry B, Vol. 119, Issue 41 https://doi.org/10.1021/acs.jpcb.5b06066	journal	September 2015
Structure and Lipid Interaction of N-Palmitoylsphingomyelin in Bilayer Membranes as Revealed by 2H-NMR Spectroscopy Mehnert, Thomas; Jacob, Kochurani; Bittman, Robert Biophysical Journal, Vol. 90, Issue 3 https://doi.org/10.1529/biophysj.105.063271	journal	February 2006
The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy Martins, Ingrid Bernardes Santana; Viegas, Taisa Giordano; dos Santos Alvares, Dayane Amino Acids, Vol. 53, Issue 5 https://doi.org/10.1007/s00726-021-02982-0	journal	April 2021
Mechanism of the Lamellar/Inverse Hexagonal Phase Transition Examined by High Resolution X-Ray Diffraction Rappolt, Michael; Hickel, Andrea; Bringezu, Frank Biophysical Journal, Vol. 84, Issue 5 https://doi.org/10.1016/s0006-3495(03)70036-8	journal	May 2003
Molecular basis for assembly of the shieldin complex and its implications for NHEJ Liang, Ling; Feng, Jiawen; Zuo, Peng Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15879-5	journal	April 2020

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Characterization of the Pseudomonas aeruginosa NQR complex, a bacterial proton pump with roles in autopoisoning resistance Raba, Daniel A.; Rosas-Lemus, Monica; Menzer, William M. Journal of Biological Chemistry, Vol. 293, Issue 40 https://doi.org/10.1074/jbc.ra118.003194	journal	August 2018
Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity Sotudeh, Noori; Morales, Paula; Hurst, Dow P. International Journal of Molecular Sciences, Vol. 20, Issue 9 https://doi.org/10.3390/ijms20092300	journal	May 2019
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields Ding, Ye; Xu, You; Qian, Cheng Journal of Computer-Aided Molecular Design, Vol. 34, Issue 4 https://doi.org/10.1007/s10822-020-00282-5	journal	January 2020
Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applications Gilmore, Sean F.; Carpenter, Timothy S.; Ingólfsson, Helgi I. Nanoscale, Vol. 10, Issue 16 https://doi.org/10.1039/c7nr09690a	journal	January 2018
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics Eastman, Peter; Swails, Jason; Chodera, John D. PLOS Computational Biology, Vol. 13, Issue 7 https://doi.org/10.1371/journal.pcbi.1005659	journal	July 2017
Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay Uba, Abdullahi Ibrahim; Yelekçi, Kemal Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 12 https://doi.org/10.1080/07391102.2017.1384402	journal	October 2017
Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments Preciado, Lina; Pereañez, Jaime; Azhagiya Singam, Ettayapuram Toxins, Vol. 10, Issue 10 https://doi.org/10.3390/toxins10100397	journal	September 2018
Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP Götz, Alexander; Högel, Philipp; Silber, Mara Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41766-1	journal	March 2019
Novel analogs of sulfasalazine as system x _c ⁻ antiporter inhibitors: Insights from the molecular modeling studies Patel, Dhavalkumar; Kharkar, Prashant S.; Gandhi, Neha S. Drug Development Research, Vol. 80, Issue 6 https://doi.org/10.1002/ddr.21557	journal	June 2019
Computer aided protein engineering to enhance the thermo-stability of CXCR1- T4 lysozyme complex Wang, Yang; Park, Jae-Hyun; Lupala, Cecylia Severin Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41838-2	journal	March 2019
Soluble klotho regulates TRPC6 calcium signaling via lipid rafts, independent of the FGFR‐FGF23 pathway Wright, Jon D.; An, Sung‐Wan; Xie, Jian The FASEB Journal, Vol. 33, Issue 8 https://doi.org/10.1096/fj.201900321r	journal	May 2019
Polarizable force field for RNA based on the classical drude oscillator: Polarizable Force Field for RNA Based on the Classical Drude Oscillator Lemkul, Justin A.; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 39, Issue 32 https://doi.org/10.1002/jcc.25709	journal	December 2018
Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji The Journal of Chemical Physics, Vol. 148, Issue 16 https://doi.org/10.1063/1.5008438	journal	April 2018
Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods Chang, Shan; Zhang, Da-Wei; Xu, Lei RNA Biology, Vol. 13, Issue 11 https://doi.org/10.1080/15476286.2016.1223007	journal	September 2016
Selectivity filter modalities and rapid inactivation of the hERG1 channel Miranda, Williams E.; DeMarco, Kevin R.; Guo, Jiqing Proceedings of the National Academy of Sciences, Vol. 117, Issue 6 https://doi.org/10.1073/pnas.1909196117	journal	January 2020
Xanthine oxidase inhibitory activity of new pyrrole carboxamide derivatives: In vitro and in silico studies Kıbrız, İbrahim Evren; Saçmacı, Mustafa; Yıldırım, İsmail Archiv der Pharmazie, Vol. 351, Issue 10 https://doi.org/10.1002/ardp.201800165	journal	August 2018
Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias Journal of Biomolecular NMR, Vol. 74, Issue 1 https://doi.org/10.1007/s10858-019-00289-7	journal	November 2019
Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs Negami, Tatsuki; Araki, Mitsugu; Okuno, Yasushi Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-53120-6	journal	November 2019
Sequential activation of STIM1 links Ca ²⁺ with luminal domain unfolding Schober, Romana; Bonhenry, Daniel; Lunz, Victoria Science Signaling, Vol. 12, Issue 608 https://doi.org/10.1126/scisignal.aax3194	journal	November 2019
β11-12 linker isomerization governs acid-sensing ion channel desensitization and recovery Rook, Matthew L.; Williamson, Abby; Lueck, John D. eLife, Vol. 9 https://doi.org/10.7554/elife.51111	journal	February 2020
Cholesterol suppresses membrane leakage by decreasing water penetrability Bu, Bing; Crowe, Michael; Diao, Jiajie Soft Matter, Vol. 14, Issue 25 https://doi.org/10.1039/c8sm00644j	journal	January 2018
Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane Hung, Huynh Minh; Hang, Tran Dieu; Nguyen, Minh Tho Proteins: Structure, Function, and Bioinformatics, Vol. 86, Issue 4 https://doi.org/10.1002/prot.25458	journal	February 2018
Brettanomyces bruxellensis SSU1 Haplotypes Confer Different Levels of Sulfite Tolerance When Expressed in a Saccharomyces cerevisiae SSU1 Null Mutant Varela, C.; Bartel, C.; Roach, M. Applied and Environmental Microbiology, Vol. 85, Issue 4 https://doi.org/10.1128/aem.02429-18	journal	December 2018
Chemical‐Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors Creutznacher, Robert; Schulze, Eric; Wallmann, Georg ChemBioChem, Vol. 21, Issue 7 https://doi.org/10.1002/cbic.201900572	journal	April 2020
L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction Errasti-Murugarren, Ekaitz; Fort, Joana; Bartoccioni, Paola Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09837-z	journal	April 2019
Potential off-target effects of beta-blockers on gut hormone receptors: In silico study including GUT-DOCK—A web service for small-molecule docking Pasznik, Pawel; Rutkowska, Ewelina; Niewieczerzal, Szymon PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210705	journal	January 2019
A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition Zeppelin, Talia; Ladefoged, Lucy Kate; Sinning, Steffen PLOS Computational Biology, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pcbi.1005907	journal	January 2018
The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations Balogh, Gábor; Komáromi, István; Bereczky, Zsuzsanna Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2019.1688194	journal	November 2019
Mutation of Ebola Virus Matrix Protein Cysteine Residues Increases Binding to Phosphatidylserine through Increased Flexibility of a Lipid Binding Loop Johnson, Kristen A.; Bhattarai, Nisha; Budicini, Melissa R. https://doi.org/10.1101/286120	preprint	March 2018
Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate Rani, R. Sandya; Saharay, Moumita RSC Advances, Vol. 9, Issue 3 https://doi.org/10.1039/c8ra08459a	journal	January 2019
Potential of Matrix Metalloproteinase Inhibitors for the Treatment of Local Tissue Damage Induced by a Type P-I Snake Venom Metalloproteinase Preciado, Lina María; Pereañez, Jaime Andrés; Comer, Jeffrey Toxins, Vol. 12, Issue 1 https://doi.org/10.3390/toxins12010008	journal	December 2019
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules: CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan Journal of Computational Chemistry, Vol. 38, Issue 21 https://doi.org/10.1002/jcc.24829	journal	May 2017
Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10 Uba, Abdullahi Ibrahim; Yelekçi, Kemal Journal of Biomolecular Structure and Dynamics, Vol. 38, Issue 15 https://doi.org/10.1080/07391102.2019.1691658	journal	November 2019
Specific Residues in a Purine Transporter Are Critical for Dimerization, ER Exit, and Function Kourkoulou, Anezia; Grevias, Pothos; Lambrinidis, George Genetics, Vol. 213, Issue 4 https://doi.org/10.1534/genetics.119.302566	journal	October 2019
Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces Osborne, Amy J.; Nan, Ruodan; Miller, Ami Journal of Biological Chemistry, Vol. 293, Issue 44 https://doi.org/10.1074/jbc.ra118.004767	journal	September 2018
New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex Ishchenko, A.; Round, E.; Borshchevskiy, V. RWTH Aachen University https://doi.org/10.18154/rwth-2017-05602	text	January 2017
Molecular dynamics simulation and binding free energy calculations of microcin J25 binding to the FhuA receptor Li, Zhenhua; Chinnasamy, Sathishkumar; Zhang, Yonghong Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2020.1751293	journal	April 2020
Anomalous behavior of membrane fluidity caused by copper-copper bond coupled phospholipids Jiang, Xiankai; Zhang, Jinjin; Zhou, Bo Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-32322-4	journal	September 2018
Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation Uba, Abdullahi Ibrahim; Weako, Jackson; Keskin, Özlem Journal of Biomolecular Structure and Dynamics https://doi.org/10.1080/07391102.2019.1615989	journal	May 2019
Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death Silvestre-Roig, Carlos; Braster, Quinte; Wichapong, Kanin Nature, Vol. 569, Issue 7755 https://doi.org/10.1038/s41586-019-1167-6	journal	May 2019
Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models Sajadi, Fatima; Rowley, Christopher N. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5472	journal	January 2018
The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1 Hofbauer, Harald F.; Gecht, Michael; Fischer, Sabine C. Journal of Cell Biology https://doi.org/10.1101/250019	posted_content	January 2018
Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components Steringer, Julia P.; Lange, Sascha; Čujová, Sabína eLife, Vol. 6 https://doi.org/10.7554/elife.28985	journal	July 2017
Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities Manzo, Giorgia; Ferguson, Philip M.; Hind, Charlotte K. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-47327-w	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 Bayel Secinti, Burcu; Tatar, Gizem; Taskin Tok, Tugba Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 9 https://doi.org/10.1080/07391102.2018.1491420	journal	October 2018
Structure of the human ClC-1 chloride channel Wang, Kaituo; Preisler, Sarah Spruce; Zhang, Liying PLOS Biology, Vol. 17, Issue 4 https://doi.org/10.1371/journal.pbio.3000218	journal	April 2019
Probing the functional conformations of an atypical proline-rich fusion peptide Dutta, Nivedita; Dutta Chowdhury, Saikat; Lahiri, Ansuman Physical Chemistry Chemical Physics, Vol. 21, Issue 37 https://doi.org/10.1039/c9cp02216c	journal	January 2019
Residue-centric modeling and design of saccharide and glycoconjugate structures Labonte, Jason W.; Adolf-Bryfogle, Jared; Schief, William R. Journal of Computational Chemistry, Vol. 38, Issue 5 https://doi.org/10.1002/jcc.24679	journal	November 2016
Distinct specific interactions of the UapA transporter with membrane lipids are critical for dimerization, ER-exit and function Kourkoulou, Anezia; Grevias, Pothos; Lambrinidis, George https://doi.org/10.1101/710897	preprint	July 2019
Molecular dynamics simulations of dihydro‐β‐erythroidine bound to the human α4β2 nicotinic acetylcholine receptor Yu, Rilei; Tae, Han‐Shen; Xu, Qingliang British Journal of Pharmacology, Vol. 176, Issue 15 https://doi.org/10.1111/bph.14698	journal	June 2019
Atomistic insight into lipid translocation by a TMEM16 scramblase Bethel, Neville P.; Grabe, Michael Proceedings of the National Academy of Sciences, Vol. 113, Issue 49 https://doi.org/10.1073/pnas.1607574113	journal	November 2016
Modelling of Ca ²⁺ -promoted structural effects in wild type and post-translationally modified Connexin26 Calligari, Paolo; Torsello, Mauro; Bortoli, Marco Molecular Simulation, Vol. 46, Issue 3 https://doi.org/10.1080/08927022.2019.1690653	journal	November 2019
Molecular modelling and simulation studies of the Mycobacterium tuberculosis multidrug efflux pump protein Rv1258c Cloete, Ruben; Kapp, Erika; Joubert, Jacques PLOS ONE, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pone.0207605	journal	November 2018
pVEC hydrophobic N-terminus is critical for antibacterial activity Alaybeyoglu, Begum; Sariyar Akbulut, Berna; Ozkirimli, Elif Journal of Peptide Science, Vol. 24, Issue 6 https://doi.org/10.1002/psc.3083	journal	May 2018
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro Journal of Computational Chemistry, Vol. 38, Issue 25 https://doi.org/10.1002/jcc.24874	journal	July 2017
Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations Sharma, Vivek; Jambrina, Pablo G.; Kaukonen, Markus Proceedings of the National Academy of Sciences, Vol. 114, Issue 48 https://doi.org/10.1073/pnas.1708628114	journal	November 2017
3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes Lopes-Rodrigues, Maximilien; Zanuy, David; Alemán, Carlos Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 15 https://doi.org/10.1080/07391102.2018.1529627	journal	December 2018
Fragment Based Molecular Dynamics for Drug Design Sessa, Lucia; Di Biasi, Luigi; Concilio, Simona Communications in Computer and Information Science https://doi.org/10.1007/978-3-319-78658-2_4	book	April 2018
Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1 Chen, Liao Y. https://doi.org/10.1101/787259	preprint	April 2019
Functional and structural analysis of rare SLC2A2 variants associated with Fanconi‐Bickel syndrome and metabolic traits Enogieru, Osatohanmwen J.; Ung, Peter M. U.; Yee, Sook Wah Human Mutation https://doi.org/10.1002/humu.23758	journal	April 2019
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems : CHARMM-GUI Qi, Yifei; Lee, Jumin; Klauda, Jeffery B. Journal of Computational Chemistry, Vol. 40, Issue 7 https://doi.org/10.1002/jcc.25773	journal	January 2019
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 Park, Soohyung; Glover, Kerney J.; Im, Wonpil Journal of Computational Chemistry, Vol. 40, Issue 16 https://doi.org/10.1002/jcc.25807	journal	March 2019
Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states Zheng, Wenjun; Wen, Han Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 10 https://doi.org/10.1002/prot.25707	journal	May 2019
Combining theoretical and experimental data to decipher CFTR 3D structures and functions Hoffmann, Brice; Elbahnsi, Ahmad; Lehn, Pierre Cellular and Molecular Life Sciences, Vol. 75, Issue 20 https://doi.org/10.1007/s00018-018-2835-7	journal	May 2018
Molecular dynamics and binding energy analysis of Vatairea guianensis lectin: a new tool for cancer studies Cavada, Benildo Sousa; Osterne, Vinicius Jose Silva; Pinto-Junior, Vanir Reis Journal of Molecular Modeling, Vol. 26, Issue 2 https://doi.org/10.1007/s00894-019-4281-3	journal	January 2020
Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist Marmolejo-Valencia, A. F.; Martínez-Mayorga, K. Journal of Computer-Aided Molecular Design, Vol. 31, Issue 5 https://doi.org/10.1007/s10822-017-0016-7	journal	March 2017
HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions Hollingsworth, Louis R.; Lemkul, Justin A.; Bevan, David R. Biophysical Journal, Vol. 115, Issue 1 https://doi.org/10.1016/j.bpj.2018.05.022	journal	July 2018
Long-Ranged Protein-Glycan Interactions Stabilize Von Willebrand Factor A2 Domain from Mechanical Unfolding Dong, Chuqiao; Lee, Jumin; Kim, Seonghoon Biophysical Journal, Vol. 116, Issue 3 https://doi.org/10.1016/j.bpj.2018.11.1054	journal	February 2019
Structural basis for selectivity and diversity in angiotensin II receptors Zhang, Haitao; Han, Gye Won; Batyuk, Alexander Nature, Vol. 544, Issue 7650 https://doi.org/10.1038/nature22035	journal	April 2017
Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand Zhang, Xianjun; Zhao, Fei; Wu, Yiran Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15383	journal	May 2017
Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism Nagarathinam, Kumar; Nakada-Nakura, Yoshiko; Parthier, Christoph Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06306-x	journal	October 2018
Molecular Mechanism of Resveratrol’s Lipid Membrane Protection Fei, Qinqin; Kent, David; Botello-Smith, Wesley M. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-18943-1	journal	January 2018
K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase Dubey, Vikas; Han, Minwoo; Kopec, Wojciech Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30885-w	journal	August 2018
Molecular Dynamics Simulations of the Allosteric Modulation of the Adenosine A2a Receptor by a Mini-G Protein Renault, Pedro; Louet, Maxime; Marie, Jacky Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41980-x	journal	April 2019
Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring Wagle, Swapnil; Georgiev, Vasil N.; Robinson, Tom Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-43418-w	journal	May 2019
An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin Faouri, Radwan Al; Krueger, Eric; Govind Kumar, Vivek Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-47725-0	journal	August 2019
Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog Kang, Xue; Elson, Christopher; Penfield, Jackson Communications Biology, Vol. 2, Issue 1 https://doi.org/10.1038/s42003-019-0653-6	journal	November 2019
Pyrithione-based ruthenium complexes as inhibitors of aldo–keto reductase 1C enzymes and anticancer agents Kljun, Jakob; Anko, Maja; Traven, Katja Dalton Transactions, Vol. 45, Issue 29 https://doi.org/10.1039/c6dt00668j	journal	January 2016
Cellulose–hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion Kumar, Rajeev; Bhagia, Samarthya; Smith, Micholas Dean Green Chemistry, Vol. 20, Issue 4 https://doi.org/10.1039/c7gc03518g	journal	January 2018
Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles Nademi, Yousef; Tang, Tian; Uludağ, Hasan Nanoscale, Vol. 12, Issue 2 https://doi.org/10.1039/c9nr08128c	journal	January 2020
Perspective: Computational modeling of accurate cellular membranes with molecular resolution Klauda, Jeffery B. The Journal of Chemical Physics, Vol. 149, Issue 22 https://doi.org/10.1063/1.5055007	journal	December 2018
Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights Hong, Lu; Vani, Bodhi P.; Thiede, Erik H. Proceedings of the National Academy of Sciences, Vol. 115, Issue 49 https://doi.org/10.1073/pnas.1812555115	journal	November 2018
Membrane perforation by the pore-forming toxin pneumolysin Vögele, Martin; Bhaskara, Ramachandra M.; Mulvihill, Estefania Proceedings of the National Academy of Sciences, Vol. 116, Issue 27 https://doi.org/10.1073/pnas.1904304116	journal	June 2019
Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells Shindou, Hideo; Koso, Hideto; Sasaki, Junko Journal of Biological Chemistry, Vol. 292, Issue 29 https://doi.org/10.1074/jbc.M117.790568	journal	July 2017
Effect of thermostable mutations on the neurotensin receptor 1 (NTSR ₁ ) activation state Nagarajan, Shanthi; Alkayed, Nabil J.; Kaul, Sanjiv Journal of Biomolecular Structure and Dynamics, Vol. 38, Issue 2 https://doi.org/10.1080/07391102.2019.1573705	journal	February 2019
The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1 Hofbauer, Harald F.; Gecht, Michael; Fischer, Sabine C. Journal of Cell Biology, Vol. 217, Issue 9 https://doi.org/10.1083/jcb.201802027	journal	June 2018
Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites Wang, Yali; Yang, Elaine; Wells, Marta M. Journal of General Physiology, Vol. 150, Issue 9 https://doi.org/10.1085/jgp.201811993	journal	July 2018
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond Balaceanu, Alexandra; Buitrago, Diana; Walther, Jürgen Nucleic Acids Research, Vol. 47, Issue 9 https://doi.org/10.1093/nar/gkz255	journal	April 2019
Modulating hinge flexibility in the APP transmembrane domain alters γ-secretase cleavage Götz, Alexander; Mylonas, Nadine; Högel, Philipp Biophysical Journal https://doi.org/10.1101/375006	posted_content	November 2018
Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations Wilson, Blake A.; Ramanathan, Arvind; Lopez, Carlos F. Biophysical Journal https://doi.org/10.1101/557744	posted_content	February 2019
An unusual amino acid substitution within hummingbird cytochrome c oxidase alters a key proton-conducting channel Dunn, Cory D.; Akpınar, Bala Anı; Sharma, Vivek G3: Genes\|Genomes\|Genetics https://doi.org/10.1101/610915	posted_content	May 2020
Membrane remodeling by the lytic fragment of sticholysin II: implications for the toroidal pore model Mesa-Galloso, H.; Valiente, P. A.; Epand, R. F. Biophysical Journal https://doi.org/10.1101/620336	posted_content	April 2019
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2 Harkey, Thomas; Kumar, Vivek Govind; Hettige, Jeevapani Scientific Reports https://doi.org/10.1101/707778	posted_content	September 2019
Systematic cysteine-crosslinking in native membranes establishes the transmembrane architecture in Ire1 clusters Väth, Kristina; Covino, Roberto; Reinhard, John Journal of Cell Biology https://doi.org/10.1101/772772	posted_content	April 2021
Oestrogenic activity of mimosine on MCF-7 breast cancer cell line through the ERα-mediated pathway Huq, AKM Moyeenul; Wai, Lam Kok; Rullah, Kamal Chemical Biology & Drug Design, Vol. 93, Issue 3 https://doi.org/10.1111/cbdd.13404	journal	October 2018
ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domain Bulla, M.; Gyimesi, G.; Kim, J. H. The Journal of Physiology, Vol. 597, Issue 2 https://doi.org/10.1113/jp277079	journal	November 2018
A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif Utesch, Tillmann; de Miguel Catalina, Alejandra; Schattenberg, Caspar mSphere, Vol. 3, Issue 5 https://doi.org/10.1128/msphere.00377-18	journal	October 2018
Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions Javanainen, Matti; Enkavi, Giray; Guixà-Gonzaléz, Ramon PLOS Computational Biology, Vol. 15, Issue 5 https://doi.org/10.1371/journal.pcbi.1007033	journal	May 2019
Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II Kemmler, Lukas; Ibrahim, Mohamed; Dobbek, Holger Freie Universität Berlin https://doi.org/10.17169/refubium-26415	text	January 2019
Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin Zhang, Wenying; Yang, Ting; Zhou, Shuangyan Biomolecules, Vol. 9, Issue 12 https://doi.org/10.3390/biom9120852	journal	December 2019
Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations Yang, Ting; Zhang, Wenying; Cheng, Jie International Journal of Molecular Sciences, Vol. 20, Issue 15 https://doi.org/10.3390/ijms20153780	journal	August 2019
Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin Preciado, Lina; Comer, Jeffrey; Núñez, Vitelbina Molecules, Vol. 23, Issue 10 https://doi.org/10.3390/molecules23102662	journal	October 2018
Identification and Characterization of NTB451 as a Potential Inhibitor of Necroptosis In, Eun-Jung; Lee, Yuno; Koppula, Sushruta Molecules, Vol. 23, Issue 11 https://doi.org/10.3390/molecules23112884	journal	November 2018
Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones Román, Juan; González, Dorian; Inostroza-Ponta, Mario Molecules, Vol. 25, Issue 4 https://doi.org/10.3390/molecules25040772	journal	February 2020
Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias Springer https://doi.org/10.5167/uzh-177033	text	January 2020
Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations Wilmes, Stephan; Hafer, Maximillian; Vuorio, Joni Zenodo https://doi.org/10.5281/zenodo.3555290	text	January 2019
The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations Balogh, Gábor; Komáromi, István; Bereczky, Zsuzsanna Taylor & Francis https://doi.org/10.6084/m9.figshare.10252967	text	January 2019
Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay Uba, Abdullahi Ibrahim; Yelekçi, Kemal Taylor & Francis https://doi.org/10.6084/m9.figshare.5527873.v1	text	January 2017
Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors Uba, Abdullahi Ibrahim; Yelekçi, Kemal Taylor & Francis https://doi.org/10.6084/m9.figshare.7571198	text	January 2019
Structural insight into the activation of a class B G-protein-coupled receptor by peptide hormones in live human cells Seidel, Lisa; Zarzycka, Barbara; Zaidi, Saheem A. eLife, Vol. 6 https://doi.org/10.7554/eLife.27711	journal	August 2017
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations Bengtsen, Tone; Holm, Viktor L.; Kjølbye, Lisbeth Ravnkilde eLife, Vol. 9 https://doi.org/10.7554/eLife.56518	journal	July 2020
CHARMM-GUI 10 years for biomolecular modeling and simulation: Biomolecular Modeling and Simulation Jo, Sunhwan; Cheng, Xi; Lee, Jumin Journal of Computational Chemistry, Vol. 38, Issue 15 https://doi.org/10.1002/jcc.24660	journal	November 2016
Novel FSHR variants causing female resistant ovary syndrome Khor, Shuzin; Lyu, Qifeng; Kuang, Yanping Molecular Genetics & Genomic Medicine, Vol. 8, Issue 2 https://doi.org/10.1002/mgg3.1082	journal	December 2019
Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra‐protein switchable motion Biggers, Laurence; Elhabashy, Hadeer; Ackad, Edward Protein Science, Vol. 29, Issue 2 https://doi.org/10.1002/pro.3780	journal	November 2019
Investigating Dual Ca2+ Modulation of the Ryanodine Receptor 1 by Molecular Dynamics Simulation Zheng, Wenjun; Wen, Han Biophysical Journal, Vol. 118, Issue 3 https://doi.org/10.1016/j.bpj.2019.11.693	journal	February 2020
Predictive compound accumulation rules yield a broad-spectrum antibiotic Richter, Michelle F.; Drown, Bryon S.; Riley, Andrew P. Nature, Vol. 545, Issue 7654 https://doi.org/10.1038/nature22308	journal	May 2017
Hydrophobic gating in BK channels Jia, Zhiguang; Yazdani, Mahdieh; Zhang, Guohui Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05970-3	journal	August 2018
An inner activation gate controls TMEM16F phospholipid scrambling Le, Trieu; Jia, Zhiguang; Le, Son C. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09778-7	journal	April 2019
Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding Dong, Chuqiao; Lee, Jumin; Kim, Seonghoon Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-34374-y	journal	October 2018
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2 Harkey, Thomas; Govind Kumar, Vivek; Hettige, Jeevapani Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-51052-9	journal	October 2019
New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex Ishchenko, A.; Round, E.; Borshchevskiy, V. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep41811	journal	February 2017
Rapid diffusion of cholesterol along polyunsaturated membranes via deep dives Javanainen, Matti; Martinez-Seara, Hector Physical Chemistry Chemical Physics, Vol. 21, Issue 22 https://doi.org/10.1039/c9cp02022e	journal	January 2019
Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding Madsen, Jesper J.; Grime, John M. A.; Rossman, Jeremy S. Proceedings of the National Academy of Sciences, Vol. 115, Issue 37 https://doi.org/10.1073/pnas.1805443115	journal	August 2018
Structural modeling of human cardiac sodium channel pore domain Ji, Xiaofeng; Xiao, Yi; Liu, Shiyong Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 9 https://doi.org/10.1080/07391102.2017.1348990	journal	July 2017
Identification of two natural compound inhibitors of Leishmania donovani Spermidine Synthase (SpdS) through molecular docking and dynamic studies V. M., Vidhya; Dubey, Vikash Kumar; Ponnuraj, Karthe Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 10 https://doi.org/10.1080/07391102.2017.1366947	journal	August 2017
Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity Manzo, Giorgia; Ferguson, Philip M.; Gustilo, V. Benjamin Scientific Reports https://doi.org/10.1101/312215	posted_content	August 2018
β11-12 linker isomerization governs Acid-sensing ion channel desensitization and recovery Rook, Matthew; Williamson, Abby; Lueck, John D. eLife https://doi.org/10.1101/746271	posted_content	August 2019
Structural analysis of phosphorylation‐associated interactions of human MCC with Scribble PDZ domains Caria, Sofia; Stewart, Bryce Z.; Jin, Ruitao The FEBS Journal, Vol. 286, Issue 24 https://doi.org/10.1111/febs.15002	journal	July 2019
Targeted fluorescence lifetime probes reveal responsive organelle viscosity and membrane fluidity Steinmark, Ida Emilie; James, Arjuna L.; Chung, Pei-Hua PLOS ONE, Vol. 14, Issue 2 https://doi.org/10.1371/journal.pone.0211165	journal	February 2019
Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding Chitongo, Rumbidzai; Obasa, Adetayo Emmanuel; Mikasi, Sello Given PLOS ONE, Vol. 15, Issue 5 https://doi.org/10.1371/journal.pone.0223464	journal	May 2020
Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane Chen, Ke; Sheng, Yuebiao; Wang, Jun International Journal of Molecular Sciences, Vol. 20, Issue 19 https://doi.org/10.3390/ijms20194760	journal	September 2019
Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay Uba, Abdullahi Ibrahim; Yelekçi, Kemal Taylor & Francis https://doi.org/10.6084/m9.figshare.5527873	text	January 2017
Conformational latitude – activity relationship of KPPR tetrapeptide analogues toward their ability to inhibit binding of vascular endothelial growth factor 165 to neuropilin‐1 Fedorczyk, Bartlomiej; Lipiński, Piotr F. J.; Tymecka, Dagmara Journal of Peptide Science, Vol. 23, Issue 6 https://doi.org/10.1002/psc.3009	journal	May 2017
Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles Doktorova, Milka; Heberle, Frederick A.; Marquardt, Drew Biophysical Journal, Vol. 116, Issue 5 https://doi.org/10.1016/j.bpj.2019.01.016	journal	March 2019
Molecular basis of PIP2-dependent regulation of the Ca2+-activated chloride channel TMEM16A Le, Son C.; Jia, Zhiguang; Chen, Jianhan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11784-8	journal	August 2019
Binding site opening by loop C shift and chloride ion-pore interaction in the GABA _A receptor model Michałowski, M. A.; Kraszewski, S.; Mozrzymas, J. W. Physical Chemistry Chemical Physics, Vol. 19, Issue 21 https://doi.org/10.1039/c7cp00582b	journal	January 2017
Na ⁺ coordination at the Na2 site of the Na ⁺ /I ⁻ symporter Ferrandino, Giuseppe; Nicola, Juan Pablo; Sánchez, Yuly E. Proceedings of the National Academy of Sciences, Vol. 113, Issue 37 https://doi.org/10.1073/pnas.1607231113	journal	August 2016
Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation Gu, Siyi; Sachleben, Joseph R.; Boughter, Christopher T. Proceedings of the National Academy of Sciences, Vol. 114, Issue 35 https://doi.org/10.1073/pnas.1707547114	journal	August 2017
Investigating dual Ca²⁺ modulation of the ryanodine receptor 1 by molecular dynamics simulation Zheng, Wenjun; Wen, Han Proteins: Structure, Function, and Bioinformatics https://doi.org/10.1101/736934	posted_content	August 2019
A two-lane mechanism for selective biological ammonium transport Williamson, Gordon; Tamburrino, Giulia; Mirandela, Gaëtan Dias Access Microbiology https://doi.org/10.1101/849562	journal	November 2019
Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus Ojennus, Deanna Dahlke; Bratt, Nicholas J.; Jones, Kent L. Acta Crystallographica Section F Structural Biology Communications, Vol. 75, Issue 10 https://doi.org/10.1107/s2053230x19011774	journal	September 2019
Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations Wilmes, Stephan; Hafer, Maximillian; Vuorio, Joni Science, Vol. 367, Issue 6478 https://doi.org/10.1126/science.aaw3242	journal	February 2020
Effect of Ca2+ on the promiscuous target-protein binding of calmodulin Westerlund, Annie M.; Delemotte, Lucie PLOS Computational Biology, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pcbi.1006072	journal	April 2018
An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel Dunn, Cory D.; Akpınar, Bala Anı; Sharma, Vivek G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 7 https://doi.org/10.1534/g3.120.401312	journal	July 2020
The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations Balogh, Gábor; Komáromi, István; Bereczky, Zsuzsanna Taylor & Francis https://doi.org/10.6084/m9.figshare.10252967.v2	text	January 2019
Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors Uba, Abdullahi Ibrahim; Yelekçi, Kemal Taylor & Francis https://doi.org/10.6084/m9.figshare.7571198.v1	text	January 2019
CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations Qi, Yifei; Lee, Jumin; Cheng, Xi Journal of Computational Chemistry, Vol. 41, Issue 5 https://doi.org/10.1002/jcc.26032	journal	July 2019
Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions Pachler, Michael; Kabelka, Ivo; Appavou, Marie-Sousai Biophysical Journal, Vol. 117, Issue 10 https://doi.org/10.1016/j.bpj.2019.10.022	journal	November 2019
Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors Ibrahim Uba, Abdullahi; Yelekçi, Kemal Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 14 https://doi.org/10.1080/07391102.2018.1521747	journal	January 2019
SurA is a “Groove-y” Chaperone That Expands Unfolded Outer Membrane Proteins Marx, Dagan C.; Plummer, Ashlee M.; Faustino, Anneliese M. Proceedings of the National Academy of Sciences https://doi.org/10.1101/2019.12.17.878660	posted_content	August 2020
Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP Götz, Alexander; Högel, Philipp; Silber, Mara Scientific Reports https://doi.org/10.1101/372698	posted_content	August 2018
Correction: A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations Alberini, Giulio; Benfenati, Fabio; Maragliano, Luca PLOS ONE, Vol. 13, Issue 2 https://doi.org/10.1371/journal.pone.0193383	journal	February 2018
Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs Kooijman, Laurens; Ansorge, Philipp; Schuster, Matthias ETH Zurich https://doi.org/10.3929/ethz-b-000382113	text	January 2020
Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models Zaka, Mehreen; Abbasi, Bilal Haider; Durdagi, Serdar Taylor & Francis https://doi.org/10.6084/m9.figshare.6866246	text	January 2018
Investigating dual Ca ²⁺ modulation of the ryanodine receptor 1 by molecular dynamics simulation Zheng, Wenjun; Wen, Han Proteins: Structure, Function, and Bioinformatics, Vol. 88, Issue 11 https://doi.org/10.1002/prot.25971	journal	July 2020
A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited Doktorova, Milka; LeVine, Michael V.; Khelashvili, George Biophysical Journal, Vol. 116, Issue 3 https://doi.org/10.1016/j.bpj.2018.12.016	journal	February 2019
Water for Sterol: an Unusual Mechanism of Sterol Egress from a StARkin Domain Khelashvili, George; Chauhan, Neha; Pandey, Kalpana Biophysical Journal, Vol. 118, Issue 3 https://doi.org/10.1016/j.bpj.2019.11.1415	journal	February 2020
Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models Zaka, Mehreen; Abbasi, Bilal Haider; Durdagi, Serdar Journal of Biomolecular Structure and Dynamics, Vol. 37, Issue 9 https://doi.org/10.1080/07391102.2018.1491423	journal	December 2018
A two-lane mechanism for selective biological ammonium transport Williamson, Gordon; Dias Mirandela, Gaetan; Tamburrino, Giulia Access Microbiology, Vol. 2, Issue 7A https://doi.org/10.1099/acmi.ac2020.po0133	journal	July 2020
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations Wieder, Marcus; Perricone, Ugo; Seidel, Thomas Monatshefte für Chemie - Chemical Monthly, Vol. 147, Issue 3 https://doi.org/10.1007/s00706-016-1674-1	journal	February 2016
Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites Pak, Alexander J.; Dannenhoffer-Lafage, Thomas; Madsen, Jesper J. Journal of Chemical Theory and Computation, Vol. 15, Issue 3 https://doi.org/10.1021/acs.jctc.8b01033	journal	January 2019
Substrate-Specific Inhibition Constants for Phospholipase A₂ Acting on Unique Phospholipid Substrates in Mixed Micelles and Membranes Using Lipidomics Mouchlis, Varnavas D.; Armando, Aaron; Dennis, Edward A. Journal of Medicinal Chemistry, Vol. 62, Issue 4 https://doi.org/10.1021/acs.jmedchem.8b01568	journal	January 2019
Unidirectional Transport Mechanism in an ATP Dependent Exporter Xu, Yanyan; Seelig, Anna; Bernèche, Simon ACS Central Science, Vol. 3, Issue 3 https://doi.org/10.1021/acscentsci.7b00068	journal	March 2017
Molecular Basis of the Glucose Transport Mechanism in Plants Selvam, Balaji; Yu, Ya-Chi; Chen, Li-Qing ACS Central Science, Vol. 5, Issue 6 https://doi.org/10.1021/acscentsci.9b00252	journal	May 2019
Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands Mohan, Rohith R.; Wilson, Mark; Gorham, Ronald D. ACS Omega, Vol. 3, Issue 6 https://doi.org/10.1021/acsomega.8b00606	journal	June 2018
Publisher Correction: Hydrophobic gating in BK channels Jia, Zhiguang; Yazdani, Mahdieh; Zhang, Guohui Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-18517-2	journal	September 2020
Asc-1 Transporter (SLC7A10): Homology Models And Molecular Dynamics Insights Into The First Steps Of The Transport Mechanism Mikou, Afaf; Cabayé, Alexandre; Goupil, Anne Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-60617-y	journal	February 2020
Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E. Chemical Science, Vol. 8, Issue 8 https://doi.org/10.1039/c7sc00980a	journal	January 2017
A functional antibody cross-reactive to both human and murine cytotoxic T-lymphocyte-associated protein 4 via binding to an N-glycosylation epitope Li, Dong; Li, Jing; Chu, Huanyu mAbs, Vol. 12, Issue 1 https://doi.org/10.1080/19420862.2020.1725365	journal	January 2020
Ensemble-based evaluation for protein structure models Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke Bioinformatics, Vol. 32, Issue 12 https://doi.org/10.1093/bioinformatics/btw262	journal	June 2016
Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study Leclerc, Fabrice; Zaccai, Giuseppe; Vergne, Jacques Scientific Reports https://doi.org/10.1101/045054	journal	March 2016
Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter Harrigan, Matthew P.; McKiernan, Keri A.; Shanmugasundaram, Veerabahu Scientific Reports https://doi.org/10.1101/092155	journal	December 2016
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane Woo, Hyeonuk; Park, Sang-Jun; Choi, Yeol Kyo Journal of Physical Chemistry https://doi.org/10.1101/2020.05.20.103325	journal	June 2020
Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level Liekkinen, Juho; de Santos Moreno, Berta; Paananen, Riku O. Frontiers in Cell and Developmental Biology https://doi.org/10.1101/2020.07.07.191569	journal	July 2020
Accelerating Dissociative Events in Molecular Dynamics Simulations by Selective Potential Scaling Deb, Indrajit; Frank, Aaron T. https://doi.org/10.1101/547307	preprint	February 2019
Effect of pressure profile of shock waves on lipid membrane deformation Kfoury, Ralph; Marzban, Bahador; Makki, Emad PLOS ONE, Vol. 14, Issue 2 https://doi.org/10.1371/journal.pone.0212566	journal	February 2019
Deciphering the Allosteric Effect of Antagonist Vismodegib on Smoothened Receptor Deactivation Using Metadynamics Simulation An, Xiaoli; Bai, Qifeng; Bai, Fang Frontiers in Chemistry, Vol. 7 https://doi.org/10.3389/fchem.2019.00406	journal	June 2019
Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor Slater, Paula G.; Gutierrez-Maldonado, Sebastian E.; Gysling, Katia Frontiers in Endocrinology, Vol. 9 https://doi.org/10.3389/fendo.2018.00043	journal	February 2018
Cannabinoid Receptor 2 Agonist JWH-015 Inhibits Interleukin-1β-Induced Inflammation in Rheumatoid Arthritis Synovial Fibroblasts and in Adjuvant Induced Arthritis Rat via Glucocorticoid Receptor Fechtner, Sabrina; Singh, Anil K.; Srivastava, Ila Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.01027	journal	May 2019
NFBTA: A Potent Cytotoxic Agent against Glioblastoma Turkez, Hasan; Nóbrega, Flávio Rogério da; Ozdemir, Ozlem Molecules, Vol. 24, Issue 13 https://doi.org/10.3390/molecules24132411	journal	June 2019
Comparison of Sampling Methods via Robust Free Energy Inference: Application to Calmodulin Westerlund, Annie M.; Harpole, Tyler J.; Blau, Christian arXiv https://doi.org/10.48550/arxiv.1704.00343	preprint	January 2017
Exchange of water for sterol underlies sterol egress from a StARkin domain Khelashvili, George; Chauhan, Neha; Pandey, Kalpana eLife, Vol. 8 https://doi.org/10.7554/elife.53444	journal	December 2019
A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters. Pujol Gimenez, Jonai; Hediger, Matthias; Gyimesi, Gergely Nature Publishing Group https://doi.org/10.7892/boris.106119	text	January 2017
ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domain Bulla, M.; Gyimesi, Gergely; Kim, Jh. Wiley-Blackwell https://doi.org/10.7892/boris.121070	text	January 2019

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