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WIREs Comput Mol Sci
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Computational Biochemistry and Biophysics

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The prospects of quantum computing in computational molecular biology

Advanced Review
Carlos Outeiral, Martin Strahm, Jiye Shi, Garrett M. Morris, Simon C. Benjamin, Charlotte M. Deane
Published Online: May 23 2020
DOI:10.1002/wcms.1481

Abstract Full article on Wiley Online Library:   HTML | PDF
Structural prediction of protein interactions and docking using conservation and coevolution

Advanced Review
Raphael Guerois, Chloé Quignot, Jessica Andreani
Published Online: May 02 2020
DOI:10.1002/wcms.1470

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico toxicology: From structure–activity relationships towards deep learning and adverse outcome pathways

Advanced Review
Jennifer Hemmerich, Gerhard F. Ecker
Published Online: Apr 01 2020
DOI:10.1002/wcms.1475

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational studies of DNA repair: Insights into the function of monofunctional DNA glycosylases in the base excision repair pathway

Focus Article
Stacey D. Wetmore, Dylan J. Nikkel, Rajwinder Kaur
Published Online: Mar 15 2020
DOI:10.1002/wcms.1471

Abstract Full article on Wiley Online Library:   HTML | PDF
P2Y1‐like nucleotide receptors—Structures, molecular modeling, mutagenesis, and oligomerization

Overview
Vigneshwaran Namasivayam, Christa E. Müller, Alexander Neumann
Published Online: Mar 04 2020
DOI:10.1002/wcms.1464

Abstract Full article on Wiley Online Library:   HTML | PDF
Ligand binding free energy and kinetics calculation in 2020

Advanced Review
Vittorio Limongelli
Published Online: Jan 10 2020
DOI:10.1002/wcms.1455

Abstract Full article on Wiley Online Library:   HTML | PDF
Interrogating chemical mechanisms in natural products biosynthesis using quantum chemical calculations

Advanced Review
Dean J. Tantillo
Published Online: Nov 20 2019
DOI:10.1002/wcms.1453

Abstract Full article on Wiley Online Library:   HTML | PDF
A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure

Advanced Review
Luca Fiorillo, Simona Bianco, Andrea Esposito, Mattia Conte, Renato Sciarretta, Francesco Musella, Andrea M. Chiariello
Published Online: Nov 16 2019
DOI:10.1002/wcms.1454

Abstract Full article on Wiley Online Library:   HTML | PDF
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

Advanced Review
Tamar Schlick, Stephanie Portillo‐Ledesma
Published Online: Aug 06 2019
DOI:10.1002/wcms.1434

Abstract Full article on Wiley Online Library:   HTML | PDF
Learning from nature: Understanding hydrogenase enzyme using computational approach

Advanced Review
Siyao Qiu, Qinye Li, Yongjun Xu, Shaohua Shen, Chenghua Sun
Published Online: May 28 2019
DOI:10.1002/wcms.1422

Abstract Full article on Wiley Online Library:   HTML | PDF
The SMFA program for quantum chemistry calculations on large molecules

Software Focus
Rika Kobayashi, Matthew A. Addicoat, Andrew T.B. Gilbert, Roger D. Amos, Michael A. Collins
Published Online: Mar 01 2019
DOI:10.1002/wcms.1413

Abstract Full article on Wiley Online Library:   HTML | PDF
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

Advanced Review
Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin
Published Online: Jan 15 2019
DOI:10.1002/wcms.1410

Abstract Full article on Wiley Online Library:   HTML | PDF
Rationalization of stereoselectivity in enzyme reactions

Advanced Review
H. C. Stephen Chan, Lu Pan, Yi Li, Shuguang Yuan
Published Online: Dec 05 2018
DOI:10.1002/wcms.1403

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular dynamics simulations of macromolecular crystals

Advanced Review
David S. Cerutti, David A. Case
Published Online: Nov 16 2018
DOI:10.1002/wcms.1402

Abstract Full article on Wiley Online Library:   HTML | PDF
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

Overview
David J. Huggins, Philip C. Biggin, Marc A. Dämgen, Jonathan W. Essex, Sarah A. Harris, Richard H. Henchman, Syma Khalid, Antonija Kuzmanic, Charles A. Laughton, Julien Michel, Adrian J. Mulholland, Edina Rosta, Mark S. P. Sansom, Marc W. van der Kamp
Published Online: Sep 27 2018
DOI:10.1002/wcms.1393

Abstract Full article on Wiley Online Library:   HTML | PDF
Electronic energy transfer in biomacromolecules

Advanced Review
Lorenzo Cupellini, Marina Corbella, Benedetta Mennucci, Carles Curutchet
Published Online: Sep 13 2018
DOI:10.1002/wcms.1392

Abstract Full article on Wiley Online Library:   HTML | PDF
Perspective on computational simulations of glycosaminoglycans

Overview
Umesh R. Desai, Nehru Viji Sankaranarayanan, Balaji Nagarajan
Published Online: Sep 10 2018
DOI:10.1002/wcms.1388

Abstract Full article on Wiley Online Library:   HTML | PDF
Disassembling solvation free energies into local contributions—Toward a microscopic understanding of solvation processes

Advanced Review
Matthias Heyden
Published Online: Aug 30 2018
DOI:10.1002/wcms.1390

Abstract Full article on Wiley Online Library:   HTML | PDF
Eukaryotic cell dynamics from crawlers to swimmers

Advanced Review
H. G. Othmer
Published Online: Jul 19 2018
DOI:10.1002/wcms.1376

Abstract Full article on Wiley Online Library:   HTML | PDF
Essentials of de novo protein design: Methods and applications

Advanced Review
Enrique Marcos, Daniel‐Adriano Silva
Published Online: Jul 17 2018
DOI:10.1002/wcms.1374

Abstract Full article on Wiley Online Library:   HTML | PDF
Out‐compute drug side effects: Focus on cytochrome P450 2D6 modeling

Advanced Review
Charleen G. Don, Martin Smieško
Published Online: May 03 2018
DOI:10.1002/wcms.1366

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational structure‐based drug design: Predicting target flexibility

Advanced Review
Jelisa Iglesias, Suwipa Saen‐oon, Robert Soliva, Victor Guallar
Published Online: Apr 29 2018
DOI:10.1002/wcms.1367

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

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

Abstract Full article on Wiley Online Library:   HTML | PDF
The sensing mechanism studies of the fluorescent probes with electronically excited state calculations

Advanced Review
Ke‐Li Han, Guang‐Yue Li
Published Online: Nov 17 2017
DOI:10.1002/wcms.1351

Abstract Full article on Wiley Online Library:   HTML | PDF
Water models for biomolecular simulations

Advanced Review
Saeed Izadi, Alexey V. Onufriev
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
John Z.H. Zhang, Jianing Song, Zhaoxi Sun, Yuna Yan, Linqiong Qiu
Published Online: Oct 24 2017
DOI:10.1002/wcms.1342

Abstract Full article on Wiley Online Library:   HTML | PDF
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

Advanced Review
Wei Wang, Siqin Cao, Lizhe Zhu, Xuhui Huang
Published Online: Oct 06 2017
DOI:10.1002/wcms.1343

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

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular electrostatic potentials and noncovalent interactions

Overview
Jane S. Murray, Peter Politzer
Published Online: Jul 18 2017
DOI:10.1002/wcms.1326

Abstract Full article on Wiley Online Library:   HTML | PDF
The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

Advanced Review
Dmitri G. Fedorov
Published Online: Jun 20 2017
DOI:10.1002/wcms.1322

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
About P‐glycoprotein: a new drugable domain is emerging from structural data

Focus Article
Ricardo J. Ferreira, Cátia A. Bonito, Maria José U. Ferreira, Daniel J.V.A. dos Santos
Published Online: May 04 2017
DOI:10.1002/wcms.1316

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
Rigidity theory for biomolecules: concepts, software, and applications

Advanced Review
Susanne M.A. Hermans, Christopher Pfleger, Christina Nutschel, Christian A. Hanke, Holger Gohlke
Published Online: Apr 27 2017
DOI:10.1002/wcms.1311

Abstract Full article on Wiley Online Library:   HTML | PDF
Polarizable force field development for lipids and their efficient applications in membrane proteins

Overview
Huiying Chu, Liaoran Cao, Xiangda Peng, Guohui Li
Published Online: Apr 26 2017
DOI:10.1002/wcms.1312

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

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

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
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Overview
Sérgio Filipe Sousa, António J. M. Ribeiro, Rui P. P. Neves, Natércia F. Brás, Nuno M. F. S. A. Cerqueira, Pedro A. Fernandes, Maria João Ramos
Published Online: Sep 01 2016
DOI:10.1002/wcms.1281

Abstract Full article on Wiley Online Library:   HTML | PDF
Optimal reaction coordinates

Advanced Review
Polina V. Banushkina, Sergei V. Krivov
Published Online: Aug 10 2016
DOI:10.1002/wcms.1276

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

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

Abstract Full article on Wiley Online Library:   HTML | PDF
Coarse‐grained models for studying protein diffusion along DNA

Advanced Review
Arnab Bhattacherjee, Dana Krepel, Yaakov Levy
Published Online: Apr 27 2016
DOI:10.1002/wcms.1262

Abstract Full article on Wiley Online Library:   HTML | PDF
Atomistic molecular dynamics simulations of ATP‐binding cassette transporters

Overview
Hui Liu, Dan Li, Youyong Li, Tingjun Hou
Published Online: Jan 22 2016
DOI:10.1002/wcms.1247

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

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

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
Computational estimation of pKa values

Overview
Paul G. Seybold, George C. Shields
Published Online: Mar 24 2015
DOI:10.1002/wcms.1218

Abstract Full article on Wiley Online Library:   HTML | PDF
Exploiting the potential energy landscape to sample free energy

Overview
Andrew J. Ballard, Stefano Martiniani, Jacob D. Stevenson, Sandeep Somani, David J. Wales
Published Online: Mar 20 2015
DOI:10.1002/wcms.1217

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
Structural modeling from electron microscopy data

Advanced Review
José Ramón López‐Blanco, Pablo Chacón
Published Online: Sep 15 2014
DOI:10.1002/wcms.1199

Abstract Full article on Wiley Online Library:   HTML | PDF
Software for predicting the 3D structure of RNA molecules

Software Focus
David Dufour, Marc A. Marti‐Renom
Published Online: Sep 09 2014
DOI:10.1002/wcms.1198

Abstract Full article on Wiley Online Library:   HTML | PDF
Reversing cancer multidrug resistance: insights into the efflux by ABC transports from in silico studies

Advanced Review
Daniel J. V. A. dos Santos, Maria‐José U. Ferreira, Ricardo J. Ferreira
Published Online: Aug 18 2014
DOI:10.1002/wcms.1196

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
The many faces of halogen bonding: a review of theoretical models and methods

Advanced Review
Sebastian Kozuch, F. Matthias Bickelhaupt, William L. Jorgensen, Mariela J. Pavan, Patric Schyman, Lando P. Wolters
Published Online: Jun 09 2014
DOI:10.1002/wcms.1189

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
Tautomerism in nucleic acid bases and base pairs: a brief overview

Overview
Manoj K. Shukla, Jerzy Leszczynski
Published Online: Feb 22 2013
DOI:10.1002/wcms.1145

Abstract Full article on Wiley Online Library:   HTML | PDF
Prediction of protein binding sites and hot spots

Advanced Review
Juan Fernández‐Recio
Published Online: May 03 2011
DOI:10.1002/wcms.45

Abstract Full article on Wiley Online Library:   HTML | PDF
The atomistic simulation of DNA

Overview
Charles A. Laughton, Sarah A. Harris
Published Online: Apr 19 2011
DOI:10.1002/wcms.46

Abstract Full article on Wiley Online Library:   HTML | PDF
Outstanding challenges in protein–ligand docking and structure‐based virtual screening

Advanced Review
Emanuela Gancia, David E. Clark, Bohdan Waszkowycz
Published Online: Mar 16 2011
DOI:10.1002/wcms.18

Abstract Full article on Wiley Online Library:   HTML | PDF
The quantum chemical cluster approach for modeling enzyme reactions

Overview
Per E.M. Siegbahn, Fahmi Himo
Published Online: Mar 10 2011
DOI:10.1002/wcms.13

Abstract Full article on Wiley Online Library:   HTML | PDF
Low‐resolution structural approaches to study biomolecular assemblies

Overview
Pau Bernadó
Published Online: Feb 18 2011
DOI:10.1002/wcms.15

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
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins

Advanced Review
Victor Guallar, Frank H. Wallrapp
Published Online: Feb 01 2011
DOI:10.1002/wcms.27

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
Noncovalent interactions in biochemistry

Overview
Kevin E. Riley, Pavel Hobza
Published Online: Jan 21 2011
DOI:10.1002/wcms.8

Abstract Full article on Wiley Online Library:   HTML | PDF
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