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WIREs Comput Mol Sci
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Simulation Methods

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Reaction coordinates and transition states in enzymatic catalysis

Advanced Review
Kirill Zinovjev, Iñaki Tuñón
Published Online: Sep 04 2017
DOI:10.1002/wcms.1329

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrative approaches in HIV ‐1 non‐nucleoside reverse transcriptase inhibitor design

Overview
Vasanthanathan Poongavanam, Vigneshwaran Namasivayam, Murugesan Vanangamudi, Hadi Al Shamaileh, Rakesh N Veedu, Jan Kihlberg, N Arul Murugan
Published Online: Aug 30 2017
DOI:10.1002/wcms.1328

Abstract Full article on Wiley Online Library:   HTML | PDF
Recent advances in dynamic docking for drug discovery

Opinion
Marco De Vivo, Andrea Cavalli
Published Online: Jun 13 2017
DOI:10.1002/wcms.1320

Abstract Full article on Wiley Online Library:   HTML | PDF
Protein design: from computer models to artificial intelligence

Advanced Review
Antonella Paladino, Filippo Marchetti, Silvia Rinaldi, Giorgio Colombo
Published Online: May 24 2017
DOI:10.1002/wcms.1318

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular ‘time‐machines’ to unravel key biological events for drug design

Overview
Aravindhan Ganesan, Michelle L. Coote, Khaled Barakat
Published Online: May 02 2017
DOI:10.1002/wcms.1306

Abstract Full article on Wiley Online Library:   HTML | PDF
Accelerating physical simulations of proteins by leveraging external knowledge

Advanced Review
Alberto Perez, Joseph A. Morrone, Ken A. Dill
Published Online: Apr 19 2017
DOI:10.1002/wcms.1309

Abstract Full article on Wiley Online Library:   HTML | PDF
Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here?

Advanced Review
Adam W. Duster, Chun‐Hung Wang, Christina M. Garza, Danielle E. Miller, Hai Lin
Published Online: Apr 17 2017
DOI:10.1002/wcms.1310

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational protein structure refinement: almost there, yet still so far to go

Advanced Review
Michael Feig
Published Online: Mar 28 2017
DOI:10.1002/wcms.1307

Abstract Full article on Wiley Online Library:   HTML | PDF
Using PyMOL as a platform for computational drug design

Software Focus
Shuguang Yuan, H.C. Stephen Chan, Zhenquan Hu
Published Online: Jan 05 2017
DOI:10.1002/wcms.1298

Abstract Full article on Wiley Online Library:   HTML | PDF
Organic–inorganic interface simulation for new material discoveries

Overview
Sathish Kumar Ramakrishnan, Jie Zhu, Csilla Gergely
Published Online: Sep 01 2016
DOI:10.1002/wcms.1277

Abstract Full article on Wiley Online Library:   HTML | PDF
Adaptive quantum mechanics/molecular mechanics methods

Advanced Review
Min Zheng, Mark P. Waller
Published Online: Apr 28 2016
DOI:10.1002/wcms.1255

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?

Advanced Review
Christin Rakers, Marcel Bermudez, Bettina G. Keller, Jérémie Mortier, Gerhard Wolber
Published Online: Jul 27 2015
DOI:10.1002/wcms.1222

Abstract Full article on Wiley Online Library:   HTML | PDF
GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Software Focus
Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, Yuji Sugita
Published Online: May 07 2015
DOI:10.1002/wcms.1220

Abstract Full article on Wiley Online Library:   HTML | PDF
Polarizable force fields for molecular dynamics simulations of biomolecules

Overview
Christopher M. Baker
Published Online: Jan 26 2015
DOI:10.1002/wcms.1215

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiresolution calculation of ionic liquids

Overview
Barbara Kirchner, Oldamur Hollóczki, José Nuno Canongia Lopes, Agílio A. H. Pádua
Published Online: Dec 05 2014
DOI:10.1002/wcms.1212

Abstract Full article on Wiley Online Library:   HTML | PDF
Direct methods for computing single‐molecule entropies from molecular simulations

Advanced Review
Dimas Suárez, Natalia Díaz
Published Online: Jul 25 2014
DOI:10.1002/wcms.1195

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular dynamics out of equilibrium: mechanics and measurables

Advanced Review
Rigoberto Hernandez, Alexander V. Popov
Published Online: Jul 15 2014
DOI:10.1002/wcms.1190

Abstract Full article on Wiley Online Library:   HTML | PDF
Computing protein dynamics from protein structure with elastic network models

Advanced Review
Ugo Bastolla
Published Online: Apr 18 2014
DOI:10.1002/wcms.1186

Abstract Full article on Wiley Online Library:   HTML | PDF
Predicting enzymatic reactivity: from theory to design

Advanced Review
Katarzyna Świderek, Iñaki Tuñón, Vicent Moliner
Published Online: Oct 08 2013
DOI:10.1002/wcms.1173

Abstract Full article on Wiley Online Library:   HTML | PDF
Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation

Advanced Review
Christopher M. Baker, Robert B. Best
Published Online: Aug 27 2013
DOI:10.1002/wcms.1167

Abstract Full article on Wiley Online Library:   HTML | PDF
The power of coarse graining in biomolecular simulations

Advanced Review
Helgi I. Ingólfsson, Cesar A. Lopez, Jaakko J. Uusitalo, Djurre H. de Jong, Srinivasa M. Gopal, Xavier Periole, Siewert J. Marrink
Published Online: Aug 27 2013
DOI:10.1002/wcms.1169

Abstract Full article on Wiley Online Library:   HTML | PDF
Symmetry‐adapted perturbation theory based on density functional theory for noncovalent interactions

Advanced Review
Georg Jansen
Published Online: Aug 22 2013
DOI:10.1002/wcms.1164

Abstract Full article on Wiley Online Library:   HTML | PDF
Frontiers in free‐energy calculations of biological systems

Advanced Review
Christophe Chipot
Published Online: Jun 06 2013
DOI:10.1002/wcms.1157

Abstract Full article on Wiley Online Library:   HTML | PDF
Coarse‐grained methods for polymeric materials: enthalpy‐ and entropy‐driven models

Overview
Paola Carbone, Carlos Avendaño
Published Online: May 10 2013
DOI:10.1002/wcms.1149

Abstract Full article on Wiley Online Library:   HTML | PDF
High‐throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure

Overview
Adam Hospital, Josep Ll Gelpi
Published Online: Feb 07 2013
DOI:10.1002/wcms.1142

Abstract Full article on Wiley Online Library:   HTML | PDF
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