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Title: Using collective variables to drive molecular dynamics simulations

Abstract

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

Authors:
 [1];  [1];  [2]
+ Show Author Affiliations
  1. Temple Univ., Philadelphia, PA (United States). Dept. of Chemistry and Institute for Computational Molecular Science
  2. National Centre for Scientific Research (CNRS), Paris (France). Lab. de Biochimie Th´eorique, Inst. de Biologie Physico-Chimique,
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1565184
Resource Type:
Accepted Manuscript
Journal Name:
Molecular Physics
Additional Journal Information:
Journal Volume: 111; Journal Issue: 22-23; Journal ID: ISSN 0026-8976
Publisher:
Taylor & Francis
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; Chemistry; Physics

Citation Formats

Fiorin, Giacomo, Klein, Michael L., and Hénin, Jérôme. Using collective variables to drive molecular dynamics simulations. United States: N. p., 2013. Web. doi:10.1080/00268976.2013.813594.
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Fiorin, Giacomo, Klein, Michael L., & Hénin, Jérôme. Using collective variables to drive molecular dynamics simulations. United States. https://doi.org/10.1080/00268976.2013.813594
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Fiorin, Giacomo, Klein, Michael L., and Hénin, Jérôme. Sat . "Using collective variables to drive molecular dynamics simulations". United States. https://doi.org/10.1080/00268976.2013.813594. https://www.osti.gov/servlets/purl/1565184.
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@article{osti_1565184,
title = {Using collective variables to drive molecular dynamics simulations},
author = {Fiorin, Giacomo and Klein, Michael L. and Hénin, Jérôme},
abstractNote = {A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.},
doi = {10.1080/00268976.2013.813594},
journal = {Molecular Physics},
number = 22-23,
volume = 111,
place = {United States},
year = {Sat Jul 06 00:00:00 EDT 2013},
month = {Sat Jul 06 00:00:00 EDT 2013}
}
Copy to clipboard
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https://doi.org/10.1080/00268976.2013.813594
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Works referenced in this record:

Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain
journal, July 2010

  • Brannigan, G.; LeBard, D. N.; Henin, J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 32
  • DOI: 10.1073/pnas.1008534107

Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
journal, June 1994

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
journal, May 2002

  • Fukunishi, Hiroaki; Watanabe, Osamu; Takada, Shoji
  • The Journal of Chemical Physics, Vol. 116, Issue 20
  • DOI: 10.1063/1.1472510

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977

Hand-Eye Calibration Using Dual Quaternions
journal, March 1999

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
journal, December 2008

  • Zheng, L.; Chen, M.; Yang, W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 51
  • DOI: 10.1073/pnas.0810631106

Serial Replica Exchange
journal, February 2007

  • Hagen, Morten; Kim, Byungchan; Liu, Pu
  • The Journal of Physical Chemistry B, Vol. 111, Issue 6
  • DOI: 10.1021/jp064479e

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
journal, December 1992

  • Rappe, A. K.; Casewit, C. J.; Colwell, K. S.
  • Journal of the American Chemical Society, Vol. 114, Issue 25, p. 10024-10035
  • DOI: 10.1021/ja00051a040

Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories
journal, April 2008

  • Sezer, Deniz; Freed, Jack H.; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 128, Issue 16
  • DOI: 10.1063/1.2908075

Software news and updates carma: A molecular dynamics analysis program
journal, January 2006

  • Glykos, Nicholas M.
  • Journal of Computational Chemistry, Vol. 27, Issue 14
  • DOI: 10.1002/jcc.20482

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

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
journal, December 2009

  • Hénin, Jérome; Fiorin, Giacomo; Chipot, Christophe
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 1
  • DOI: 10.1021/ct9004432

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements
journal, December 2009

  • Alemani, Davide; Collu, Francesca; Cascella, Michele
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 1
  • DOI: 10.1021/ct900457z

GROMACS 3.0: a package for molecular simulation and trajectory analysis
journal, August 2001

  • Lindahl, Erik; Hess, Berk; van der Spoel, David
  • Journal of Molecular Modeling, Vol. 7, Issue 8
  • DOI: 10.1007/s008940100045

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
journal, February 2009

  • Deng, Yuqing; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 113, Issue 8
  • DOI: 10.1021/jp807701h

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

Statistical Mechanical Theory of Transport Processes. VII. The Coefficient of Thermal Conductivity of Monatomic Liquids
journal, May 1954

  • Zwanzig, Robert W.; Kirkwood, John G.; Oppenheim, Irwin
  • The Journal of Chemical Physics, Vol. 22, Issue 5
  • DOI: 10.1063/1.1740193

A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
journal, July 2006

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Velocity Verlet algorithm for dissipative-particle-dynamics-based models of suspensions
journal, March 1999

Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules
journal, June 2005

  • Kamberaj, H.; Low, R. J.; Neal, M. P.
  • The Journal of Chemical Physics, Vol. 122, Issue 22
  • DOI: 10.1063/1.1906216

Exploring protein native states and large-scale conformational changes with a modified generalized born model
journal, March 2004

  • Onufriev, Alexey; Bashford, Donald; Case, David A.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 55, Issue 2
  • DOI: 10.1002/prot.20033

Using quaternions to calculate RMSD
journal, January 2004

  • Coutsias, Evangelos A.; Seok, Chaok; Dill, Ken A.
  • Journal of Computational Chemistry, Vol. 25, Issue 15
  • DOI: 10.1002/jcc.20110

Energy landscape of a small peptide revealed by dihedral angle principal component analysis
journal, November 2004

  • Mu, Yuguang; Nguyen, Phuong H.; Stock, Gerhard
  • Proteins: Structure, Function, and Bioinformatics, Vol. 58, Issue 1
  • DOI: 10.1002/prot.20310

An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles
journal, January 2002

Replica-exchange molecular dynamics method for protein folding
journal, November 1999

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
journal, May 1995

  • Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
  • Journal of the American Chemical Society, Vol. 117, Issue 19
  • DOI: 10.1021/ja00124a002

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
journal, February 2012

  • Zheng, Lianqing; Yang, Wei
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 3
  • DOI: 10.1021/ct200726v

PLUMED: A portable plugin for free-energy calculations with molecular dynamics
journal, October 2009

  • Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni
  • Computer Physics Communications, Vol. 180, Issue 10
  • DOI: 10.1016/j.cpc.2009.05.011

Finding Transition Pathways Using the String Method with Swarms of Trajectories
journal, March 2008

  • Pan, Albert C.; Sezer, Deniz; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 112, Issue 11
  • DOI: 10.1021/jp0777059

Asynchronous replica exchange for molecular simulations
journal, January 2008

  • Gallicchio, Emilio; Levy, Ronald M.; Parashar, Manish
  • Journal of Computational Chemistry, Vol. 29, Issue 5
  • DOI: 10.1002/jcc.20839

Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
journal, October 2006

  • Bussi, Giovanni; Gervasio, Francesco Luigi; Laio, Alessandro
  • Journal of the American Chemical Society, Vol. 128, Issue 41
  • DOI: 10.1021/ja062463w

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
journal, January 1996

  • Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
  • Journal of the American Chemical Society, Vol. 118, Issue 45
  • DOI: 10.1021/ja9621760

Molecular dynamics simulation using quaternions
journal, September 1985

Computing time scales from reaction coordinates by milestoning
journal, June 2004

  • Faradjian, Anton K.; Elber, Ron
  • The Journal of Chemical Physics, Vol. 120, Issue 23
  • DOI: 10.1063/1.1738640

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
journal, June 2004

  • Hamelberg, Donald; Mongan, John; McCammon, J. Andrew
  • The Journal of Chemical Physics, Vol. 120, Issue 24
  • DOI: 10.1063/1.1755656

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
journal, January 2008

Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics
journal, September 2005

  • Ciccotti, Giovanni; Kapral, Raymond; Vanden-Eijnden, Eric
  • ChemPhysChem, Vol. 6, Issue 9
  • DOI: 10.1002/cphc.200400669

Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
journal, August 1982

  • Lipari, Giovanni; Szabo, Attila
  • Journal of the American Chemical Society, Vol. 104, Issue 17
  • DOI: 10.1021/ja00381a009

Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants
journal, January 2007

Multidimensional replica-exchange method for free-energy calculations
journal, October 2000

  • Sugita, Yuji; Kitao, Akio; Okamoto, Yuko
  • The Journal of Chemical Physics, Vol. 113, Issue 15
  • DOI: 10.1063/1.1308516

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
journal, March 2010

  • Abrams, C. F.; Vanden-Eijnden, E.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 11
  • DOI: 10.1073/pnas.0914540107

A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
journal, November 1990

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling
journal, August 2009

  • Rauscher, Sarah; Neale, Chris; Pomès, Régis
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 10
  • DOI: 10.1021/ct900302n

Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates
journal, May 2000

  • den Otter, W. K.
  • The Journal of Chemical Physics, Vol. 112, Issue 17
  • DOI: 10.1063/1.481329

Molecular dynamics study of unbinding of the avidin-biotin complex
journal, April 1997

Essential dynamics of proteins
journal, December 1993

  • Amadei, Andrea; Linssen, Antonius B. M.; Berendsen, Herman J. C.
  • Proteins: Structure, Function, and Genetics, Vol. 17, Issue 4
  • DOI: 10.1002/prot.340170408

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics †
journal, March 2006

  • Raiteri, Paolo; Laio, Alessandro; Gervasio, Francesco Luigi
  • The Journal of Physical Chemistry B, Vol. 110, Issue 8
  • DOI: 10.1021/jp054359r

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
journal, January 2001

  • Schuler, Lukas D.; Daura, Xavier; van Gunsteren, Wilfred F.
  • Journal of Computational Chemistry, Vol. 22, Issue 11
  • DOI: 10.1002/jcc.1078

Computation of free energy profiles with parallel adaptive dynamics
journal, April 2007

  • Lelièvre, Tony; Rousset, Mathias; Stoltz, Gabriel
  • The Journal of Chemical Physics, Vol. 126, Issue 13
  • DOI: 10.1063/1.2711185

Symplectic quaternion scheme for biophysical molecular dynamics
journal, May 2002

  • Miller, T. F.; Eleftheriou, M.; Pattnaik, P.
  • The Journal of Chemical Physics, Vol. 116, Issue 20
  • DOI: 10.1063/1.1473654

Overcoming free energy barriers using unconstrained molecular dynamics simulations
journal, August 2004

  • Hénin, Jérôme; Chipot, Christophe
  • The Journal of Chemical Physics, Vol. 121, Issue 7
  • DOI: 10.1063/1.1773132

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars
journal, February 2008

  • Akimov, Alexei V.; Nemukhin, Alexander V.; Moskovsky, Alexander A.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 4
  • DOI: 10.1021/ct7002594

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
journal, November 2012

  • Gumbart, James C.; Roux, Benoît; Chipot, Christophe
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct3008099

A method for accelerating the molecular dynamics simulation of infrequent events
journal, March 1997

  • Voter, Arthur F.
  • The Journal of Chemical Physics, Vol. 106, Issue 11
  • DOI: 10.1063/1.473503

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

Dihedral angle principal component analysis of molecular dynamics simulations
journal, June 2007

  • Altis, Alexandros; Nguyen, Phuong H.; Hegger, Rainer
  • The Journal of Chemical Physics, Vol. 126, Issue 24
  • DOI: 10.1063/1.2746330

Local elevation: A method for improving the searching properties of molecular dynamics simulation
journal, December 1994

  • Huber, Thomas; Torda, Andrew E.; van Gunsteren, Wilfred F.
  • Journal of Computer-Aided Molecular Design, Vol. 8, Issue 6
  • DOI: 10.1007/BF00124016

Escaping free-energy minima
journal, September 2002

  • Laio, A.; Parrinello, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.202427399

A Bias-Exchange Approach to Protein Folding
journal, May 2007

  • Piana, Stefano; Laio, Alessandro
  • The Journal of Physical Chemistry B, Vol. 111, Issue 17
  • DOI: 10.1021/jp067873l

A discussion of the solution for the best rotation to relate two sets of vectors
journal, September 1978

Adaptive biasing force method for scalar and vector free energy calculations
journal, April 2008

  • Darve, Eric; Rodríguez-Gómez, David; Pohorille, Andrew
  • The Journal of Chemical Physics, Vol. 128, Issue 14
  • DOI: 10.1063/1.2829861

Calculating free energies using average force
journal, November 2001

  • Darve, Eric; Pohorille, Andrew
  • The Journal of Chemical Physics, Vol. 115, Issue 20
  • DOI: 10.1063/1.1410978

Statistical Mechanics of Fluid Mixtures
journal, May 1935

  • Kirkwood, John G.
  • The Journal of Chemical Physics, Vol. 3, Issue 5
  • DOI: 10.1063/1.1749657

Predicting slow structural transitions in macromolecular systems: Conformational flooding
journal, September 1995

Transition path sampling and the calculation of rate constants
journal, February 1998

  • Dellago, Christoph; Bolhuis, Peter G.; Csajka, Félix S.
  • The Journal of Chemical Physics, Vol. 108, Issue 5
  • DOI: 10.1063/1.475562

Ceftazidime is a potential drug to inhibit SARS-CoV-2 infection in vitro by blocking spike protein–ACE2 interaction
journal, May 2021

  • Lin, ChangDong; Li, Yue; Zhang, YueBin
  • Signal Transduction and Targeted Therapy, Vol. 6, Issue 1
  • DOI: 10.1038/s41392-021-00619-y

Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
text, January 2003

  • Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele
  • American Physical Society
  • DOI: 10.5167/uzh-138232

Large-Scale Conformational Sampling of Proteins Using Temperature-Accelerated Molecular Dynamics
journal, January 2010

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
text, January 2008

PLUMED: a portable plugin for free-energy calculations with molecular dynamics
text, January 2009

Multidimensional replica-exchange method for free-energy calculations
text, January 2000

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    • Terenzi, Alessio; Gattuso, Hugo; Spinello, Angelo
    • Antioxidants, Vol. 8, Issue 10
    • DOI: 10.3390/antiox8100472

    Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
    journal, December 2013

    Energy Landscapes of Ligand Motion Inside the Tunnel-Like Cavity of Lipid Transfer Proteins: The Case of the Pru p 3 Allergen
    journal, March 2019

    • Cuevas-Zuviría, Bruno; Garrido-Arandia, María; Díaz-Perales, Araceli
    • International Journal of Molecular Sciences, Vol. 20, Issue 6
    • DOI: 10.3390/ijms20061432

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

    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

    Predicting NRTL binary interaction parameters from molecular simulations
    journal, February 2018

    • Ravichandran, Ashwin; Khare, Rajesh; Chen, Chau-Chyun
    • AIChE Journal, Vol. 64, Issue 7
    • DOI: 10.1002/aic.16117

    Host-Guest [2+2] Cycloaddition Reaction: Postsynthetic Modulation of CO 2 Selectivity and Magnetic Properties in a Bimodal Metal-Organic Framework
    journal, April 2016

    • Hazra, Arpan; Bonakala, Satyanarayana; Bejagam, Karteek K.
    • Chemistry - A European Journal, Vol. 22, Issue 23
    • DOI: 10.1002/chem.201505131

    Interplay of cysteine exposure and global protein dynamics in small‐molecule recognition by a regulator of G‐protein signaling protein
    journal, December 2018

    • Mohammadi, Mohammadjavad; Mohammadiarani, Hossein; Shaw, Vincent S.
    • Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 2
    • DOI: 10.1002/prot.25642

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

    Automated design of collective variables using supervised machine learning
    journal, September 2018

    • Sultan, Mohammad M.; Pande, Vijay S.
    • The Journal of Chemical Physics, Vol. 149, Issue 9
    • DOI: 10.1063/1.5029972

    Calculations of free energy of surface interactions in crystalline polyethylene
    journal, July 2018

    • Yeh, In-Chul; Andzelm, Jan W.
    • The Journal of Chemical Physics, Vol. 149, Issue 1
    • DOI: 10.1063/1.5031026

    Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K ions
    journal, December 2018

    • Sharawy, Mahmoud; Consta, Styliani
    • The Journal of Chemical Physics, Vol. 149, Issue 22
    • DOI: 10.1063/1.5050534

    Principal component analysis of nonequilibrium molecular dynamics simulations
    journal, May 2019

    • Post, Matthias; Wolf, Steffen; Stock, Gerhard
    • The Journal of Chemical Physics, Vol. 150, Issue 20
    • DOI: 10.1063/1.5089636

    Computing committor functions for the study of rare events using deep learning
    journal, August 2019

    • Li, Qianxiao; Lin, Bo; Ren, Weiqing
    • The Journal of Chemical Physics, Vol. 151, Issue 5
    • DOI: 10.1063/1.5110439

    Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP
    journal, February 2019

    • Leone, Vanessa; Waclawska, Izabela; Kossmann, Katharina
    • Journal of General Physiology, Vol. 151, Issue 3
    • DOI: 10.1085/jgp.201812111

    Structural basis of oligosaccharide processing by glycosaminoglycan sulfotransferases
    journal, June 2018

    • Gesteira, Tarsis F.; Coulson-Thomas, Vivien J.
    • Glycobiology, Vol. 28, Issue 11
    • DOI: 10.1093/glycob/cwy055

    Predicting protein functional motions: an old recipe with a new twist
    journal, January 2019

    • Grudinin, Sergei; Laine, Elodie; Hoffmann, Alexandre
    • Biophysical Journal
    • DOI: 10.1101/703652

    Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery: Structural basis for substrate selection
    journal, August 2017

    • Bamert, Rebecca S.; Lundquist, Karl; Hwang, Hyea
    • Molecular Microbiology, Vol. 106, Issue 1
    • DOI: 10.1111/mmi.13757

    Binding of the general anesthetic sevoflurane to ion channels
    journal, November 2018

    Molecular mechanisms of mesoporous silica formation from colloid solution: Ripening-reactions arrest hollow network structures
    journal, March 2019

    Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K2P Channels
    journal, January 2020

    • Bustos, Daniel; Bedoya, Mauricio; Ramírez, David
    • International Journal of Molecular Sciences, Vol. 21, Issue 2
    • DOI: 10.3390/ijms21020532

    Promoting transparency and reproducibility in enhanced molecular simulations
    text, January 2019

    • Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo
    • Nature Publishing Group
    • DOI: 10.5167/uzh-174059

    SSAGES : Software Suite for Advanced General Ensemble Simulations
    text, January 2018

    • Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian
    • American Institute of Physics (AIP)
    • DOI: 10.5445/ir/1000080598

    Molecular dynamics simulations of the interaction of phospholipid bilayers with polycaprolactone
    text, January 2019

    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

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

    Mechanistic insight into the early stages of amyloid formation using an anuran peptide
    journal, May 2019

    • Ray, Sourav; Holden, Stephanie; Martin, Lisandra L.
    • Peptide Science, Vol. 111, Issue 5
    • DOI: 10.1002/pep2.24120

    Influence of charge sequence on the adsorption of polyelectrolytes to oppositely-charged polyelectrolyte brushes
    journal, January 2019

    • Sethuraman, Vaidyanathan; McGovern, Michael; Morse, David C.
    • Soft Matter, Vol. 15, Issue 27
    • DOI: 10.1039/c9sm00581a

    In situ data analytics and indexing of protein trajectories
    journal, January 2017

    • Johnston, Travis; Zhang, Boyu; Liwo, Adam
    • Journal of Computational Chemistry, Vol. 38, Issue 16
    • DOI: 10.1002/jcc.24729

    Electrostatic Lock in the Transport Cycle of the Multidrug Resistance Transporter EmrE
    journal, February 2019

    Automated design of collective variables using supervised machine learning
    preprint, January 2018

    Computing Committor Functions for the Study of Rare Events Using Deep Learning
    text, January 2019

    Investigation on the intermolecular interactions in aliphatic isocyanurate liquids: revealing the importance of dispersion
    journal, April 2019

    The Rich Solid-State Phase Behavior of l-Phenylalanine: Disappearing Polymorphs and High Temperature Forms
    journal, January 2019

    • Cuppen, Herma M.; Smets, Mireille M. H.; Krieger, Annika M.
    • Crystal Growth & Design, Vol. 19, Issue 3
    • DOI: 10.1021/acs.cgd.8b01655

    RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
    journal, January 2018

    Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results
    journal, April 2020

    • Treece, Bradley W.; Heinrich, Frank; Ramanathan, Arvind
    • Journal of Chemical Theory and Computation, Vol. 16, Issue 5
    • DOI: 10.1021/acs.jctc.0c00136

    Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method
    journal, December 2016

    • Lesage, Adrien; Lelièvre, Tony; Stoltz, Gabriel
    • The Journal of Physical Chemistry B, Vol. 121, Issue 15
    • DOI: 10.1021/acs.jpcb.6b10055

    Promoting transparency and reproducibility in enhanced molecular simulations
    journal, July 2019

    Simple MD-based model for oxidative folding of peptides and proteins
    journal, August 2017

    • Izmailov, Sergei A.; Podkorytov, Ivan S.; Skrynnikov, Nikolai R.
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/s41598-017-09229-7

    Interrogating the conformational dynamics of BetP transport
    journal, February 2019

    Free energy calculations suggest a mechanism for Na+/K+-ATPase ion selectivity
    journal, February 2017

    • Razavi, Asghar M.; Delemotte, Lucie; Berlin, Joshua R.
    • Journal of Biological Chemistry
    • DOI: 10.1101/106724

    Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes
    journal, January 2018

    • Miguel-Escalada, Irene; Bonàs-Guarch, Silvia; Cebola, Inês
    • Nature Genetics
    • DOI: 10.1101/400291

    Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
    journal, October 2017

    Dynamics of Open DNA Sliding Clamps
    journal, May 2016

    Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function
    journal, November 2018

    Structure, Dynamics and Thermodynamics of Intruded Electrolytes in ZIF-8
    journal, April 2019

    Energy Landscapes of Ligand Motion Inside the Tunnel-Like Cavity of Lipid Transfer Proteins: The Case of the Pru p 3 Allergen
    journal, March 2019

    • Cuevas-Zuviría, Bruno; Garrido-Arandia, María; Díaz-Perales, Araceli
    • International Journal of Molecular Sciences, Vol. 20, Issue 6
    • DOI: 10.3390/ijms20061432

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

    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

    Evaluation of Ochratoxin Recognition by Peptides Using Explicit Solvent Molecular Dynamics
    journal, May 2017

    • Thyparambil, Aby A.; Bazin, Ingrid; Guiseppi-Elie, Anthony
    • Toxins, Vol. 9, Issue 5
    • DOI: 10.3390/toxins9050164

    Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin
    journal, December 2017

    • Thyparambil, Aby; Bazin, Ingrid; Guiseppi-Elie, Anthony
    • Toxins, Vol. 9, Issue 12
    • DOI: 10.3390/toxins9120395

    Role of Water Model on Ion Dissociation at Ambient Conditions
    text, January 2021

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