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WIREs Comput Mol Sci
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Molecular and Statistical Mechanics

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On flexible force fields for metal–organic frameworks: Recent developments and future prospects

Advanced Review
Jurn Heinen, David Dubbeldam
Published Online: Mar 25 2018
DOI:10.1002/wcms.1363

Abstract Full article on Wiley Online Library:   HTML | PDF
Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment

Advanced Review
Shayon Bhattacharya, Liang Xu, Damien Thompson
Published Online: Feb 13 2018
DOI:10.1002/wcms.1359

Abstract Full article on Wiley Online Library:   HTML | PDF
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
Advanced models for water simulations

Advanced Review
Omar Demerdash, Lee‐Ping Wang, Teresa Head‐Gordon
Published Online: Nov 23 2017
DOI:10.1002/wcms.1355

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
Interaction entropy for computational alanine scanning in protein–protein binding

Overview
Linqiong Qiu, Yuna Yan, Zhaoxi Sun, Jianing Song, John Z.H. Zhang
Published Online: Oct 24 2017
DOI:10.1002/wcms.1342

Abstract Full article on Wiley Online Library:   HTML | PDF
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

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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

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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
3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

Advanced Review
François Le Dily, François Serra, Marc A. Marti‐Renom
Published Online: Apr 10 2017
DOI:10.1002/wcms.1308

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
What can molecular simulation do for global warming?

Advanced Review
Ziqi Tian, Sheng Dai, De‐en Jiang
Published Online: Jan 21 2016
DOI:10.1002/wcms.1241

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling of ribonucleic acid–ligand interactions

Advanced Review
Filip Stefaniak, Ewa I. Chudyk, Michael Bodkin, Wayne K. Dawson, Janusz M. Bujnicki
Published Online: Sep 14 2015
DOI:10.1002/wcms.1226

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
Correct electrostatic treatment of noncovalent interactions: the importance of polarization

Overview
Timothy Clark, Peter Politzer, Jane S. Murray
Published Online: Dec 01 2014
DOI:10.1002/wcms.1210

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
The description of electronic processes inside proteins from Car–Parrinello molecular dynamics: chemical transformations

Overview
Carme Rovira
Published Online: May 03 2013
DOI:10.1002/wcms.1153

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
Proteins in the gas phase

Advanced Review
Tim Meyer, Valérie Gabelica, Helmut Grubmüller, Modesto Orozco
Published Online: Nov 29 2012
DOI:10.1002/wcms.1130

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
Recent successes in coarse‐grained modeling of DNA

Advanced Review
Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian
Published Online: Aug 08 2012
DOI:10.1002/wcms.1114

Abstract Full article on Wiley Online Library:   HTML | PDF
Coarse‐grained models of water

Overview
Leonardo Darré, Matías R. Machado, Sergio Pantano
Published Online: Jun 06 2012
DOI:10.1002/wcms.1097

Abstract Full article on Wiley Online Library:   HTML | PDF
Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins

Overview
Santiago Esteban‐Martín, Robert Bryn Fenwick, Xavier Salvatella
Published Online: Apr 18 2012
DOI:10.1002/wcms.1093

Abstract Full article on Wiley Online Library:   HTML | PDF
Optimization of protein models

Advanced Review
Dominik Gront, Sebastian Kmiecik, Maciej Blaszczyk, Dariusz Ekonomiuk, Andrzej Koliński
Published Online: Mar 29 2012
DOI:10.1002/wcms.1090

Abstract Full article on Wiley Online Library:   HTML | PDF
Electron transfer in DNA

Advanced Review
Khatcharin Siriwong, Alexander A. Voityuk
Published Online: Mar 29 2012
DOI:10.1002/wcms.1102

Abstract Full article on Wiley Online Library:   HTML | PDF
New advances in metadynamics

Overview
Ludovico Sutto, Simone Marsili, Francesco Luigi Gervasio
Published Online: Mar 29 2012
DOI:10.1002/wcms.1103

Abstract Full article on Wiley Online Library:   HTML | PDF
Essential dynamics: foundation and applications

Overview
Isabella Daidone, Andrea Amadei
Published Online: Feb 29 2012
DOI:10.1002/wcms.1099

Abstract Full article on Wiley Online Library:   HTML | PDF
Carbohydrate force fields

Advanced Review
B. Lachele Foley, Matthew B. Tessier, Robert J. Woods
Published Online: Oct 31 2011
DOI:10.1002/wcms.89

Abstract Full article on Wiley Online Library:   HTML | PDF
Next challenges in protein–protein docking: from proteome to interactome and beyond

Overview
Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin
Published Online: Sep 28 2011
DOI:10.1002/wcms.91

Abstract Full article on Wiley Online Library:   HTML | PDF
Recent developments and applications of the CHARMM force fields

Advanced Review
Xiao Zhu, Pedro E. M. Lopes, Alexander D. MacKerell
Published Online: Jun 28 2011
DOI:10.1002/wcms.74

Abstract Full article on Wiley Online Library:   HTML | PDF
Selected features of the polarizable continuum model for the representation of solvation

Advanced Review
Jacopo Tomasi
Published Online: Jun 03 2011
DOI:10.1002/wcms.54

Abstract Full article on Wiley Online Library:   HTML | PDF
Umbrella sampling

Advanced Review
Johannes Kästner
Published Online: May 26 2011
DOI:10.1002/wcms.66

Abstract Full article on Wiley Online Library:   HTML | PDF
The COSMO and COSMO‐RS solvation models

Advanced Review
Andreas Klamt
Published Online: Apr 28 2011
DOI:10.1002/wcms.56

Abstract Full article on Wiley Online Library:   HTML | PDF
Proline‐derived organocatalysis and synergism between theory and experiments

Overview
Raghavan B. Sunoj
Published Online: Apr 15 2011
DOI:10.1002/wcms.37

Abstract Full article on Wiley Online Library:   HTML | PDF
Cation–π and anion–π interactions

Advanced Review
Antonio Frontera, David Quiñonero, Pere M. Deyà
Published Online: Apr 11 2011
DOI:10.1002/wcms.14

Abstract Full article on Wiley Online Library:   HTML | PDF
Cooperative dynamics of proteins unraveled by network models

Overview
Eran Eyal, Anindita Dutta, Ivet Bahar
Published Online: Apr 11 2011
DOI:10.1002/wcms.44

Abstract Full article on Wiley Online Library:   HTML | PDF
Receptor flexibility in small‐molecule docking calculations

Advanced Review
Daria B. Kokh, Rebecca C. Wade, Wolfgang Wenzel
Published Online: Mar 17 2011
DOI:10.1002/wcms.29

Abstract Full article on Wiley Online Library:   HTML | PDF
Metadynamics

Advanced Review
Alessandro Barducci, Massimiliano Bonomi, Michele Parrinello
Published Online: Feb 18 2011
DOI:10.1002/wcms.31

Abstract Full article on Wiley Online Library:   HTML | PDF
Polarization effects in molecular interactions

Overview
F. Javier Luque, François Dehez, Christophe Chipot, Modesto Orozco
Published Online: Feb 03 2011
DOI:10.1002/wcms.32

Abstract Full article on Wiley Online Library:   HTML | PDF
Algorithm improvements for molecular dynamics simulations

Advanced Review
Per Larsson, Berk Hess, Erik Lindahl
Published Online: Jan 21 2011
DOI:10.1002/wcms.3

Abstract Full article on Wiley Online Library:   HTML | PDF
Discrete molecular dynamics

Overview
Elizabeth A. Proctor, Feng Ding, Nikolay V. Dokholyan
Published Online: Jan 21 2011
DOI:10.1002/wcms.4

Abstract Full article on Wiley Online Library:   HTML | PDF
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