Molecular Dynamics and Monte-Carlo Methods

Molecular simulations in drug delivery: Opportunities and challenges

Advanced Review
Ratna S. Katiyar, Prateek K. Jha
Published Online: Feb 01 2018
DOI:10.1002/wcms.1358

Abstract Full article on Wiley Online Library: HTML | PDF

Atomistic modeling of graphene/hexagonal boron nitride polymer nanocomposites: a review

Advanced Review
Akarsh Verma, Avinash Parashar, M. Packirisamy
Published Online: Nov 13 2017
DOI:10.1002/wcms.1346

Abstract Full article on Wiley Online Library: HTML | PDF

Water models for biomolecular simulations

Advanced Review
Alexey V. Onufriev, Saeed Izadi
Published Online: Nov 13 2017
DOI:10.1002/wcms.1347

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

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

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

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

Atomistic simulations of nucleosomes

Overview
Mithun Biswas, Jörg Langowski, Thomas C. Bishop
Published Online: Jan 31 2013
DOI:10.1002/wcms.1139

Abstract Full article on Wiley Online Library: HTML | PDF

Predictions of protein–RNA interactions

Advanced Review
Davide Cirillo, Federico Agostini, Gian Gaetano Tartaglia
Published Online: Sep 25 2012
DOI:10.1002/wcms.1119

Abstract Full article on Wiley Online Library: HTML | PDF

Resonance energy flow dynamics of coherently delocalized excitons in biological and macromolecular systems: Recent theoretical advances and open issues

Advanced Review
Seogjoo Jang, Yuan‐Chung Cheng
Published Online: Aug 08 2012
DOI:10.1002/wcms.1111

Abstract Full article on Wiley Online Library: HTML | PDF

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