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WIREs Comput Mol Sci
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Computer and Information Science

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Classical molecular dynamics on graphics processing unit architectures

Overview
Ádám Jász, Ádám Rák, István Ladjánszki, György Cserey
Published Online: Sep 05 2019
DOI:10.1002/wcms.1444

Abstract Full article on Wiley Online Library:   HTML | PDF
Making machine learning a useful tool in the accelerated discovery of transition metal complexes

Opinion
Heather J. Kulik
Published Online: Aug 02 2019
DOI:10.1002/wcms.1439

Abstract Full article on Wiley Online Library:   HTML | PDF
From machine learning to deep learning: Advances in scoring functions for protein–ligand docking

Advanced Review
Chao Shen, Junjie Ding, Zhe Wang, Dongsheng Cao, Xiaoqin Ding, Tingjun Hou
Published Online: Jun 27 2019
DOI:10.1002/wcms.1429

Abstract Full article on Wiley Online Library:   HTML | PDF
Formatting biological big data for modern machine learning in drug discovery

Advanced Review
Patrick Aloy, Martino Bertoni, Adrià Fernández‐Torras, Miquel Duran‐Frigola
Published Online: Dec 27 2018
DOI:10.1002/wcms.1408

Abstract Full article on Wiley Online Library:   HTML | PDF
Advances and challenges in deep generative models for de novo molecule generation

Opinion
Qi Liu, Jing Yu, Aizong Shen, Sheng Qu, Guohui Chuai, Zhaoyi Yang, Yukang Gong, Dongyu Xue
Published Online: Oct 19 2018
DOI:10.1002/wcms.1395

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

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

Abstract Full article on Wiley Online Library:   HTML | PDF
Ab initio computations of molecular systems by the auxiliary‐field quantum Monte Carlo method

Advanced Review
Mario Motta, Shiwei Zhang
Published Online: May 25 2018
DOI:10.1002/wcms.1364

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico toxicology: comprehensive benchmarking of multi‐label classification methods applied to chemical toxicity data

Advanced Review
Arwa B. Raies, Vladimir B. Bajic
Published Online: Dec 04 2017
DOI:10.1002/wcms.1352

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
Energy decomposition analysis

Advanced Review
Gernot Frenking, Diego M. Andrada, Moritz von Hopffgarten, Lili Zhao
Published Online: Nov 10 2017
DOI:10.1002/wcms.1345

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
Recent advances in the prediction of non‐CYP450‐mediated drug metabolism

Advanced Review
Vaibhav A. Dixit, L. Arun Lal, Simran R. Agrawal
Published Online: Jun 02 2017
DOI:10.1002/wcms.1323

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
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
Objective review of de novo stand‐alone error correction methods for NGS data

Advanced Review
Andy S. Alic, David Ruzafa, Joaquin Dopazo, Ignacio Blanquer
Published Online: Jan 11 2016
DOI:10.1002/wcms.1239

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico toxicology: computational methods for the prediction of chemical toxicity

Advanced Review
Arwa B. Raies, Vladimir B. Bajic
Published Online: Jan 06 2016
DOI:10.1002/wcms.1240

Abstract Full article on Wiley Online Library:   HTML | PDF
Structure and water oxidation activity of 3d metal oxides

Advanced Review
Zhi‐Pan Liu, Ye‐Fei Li
Published Online: Dec 28 2015
DOI:10.1002/wcms.1236

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
Communications on quantum similarity (4): collective distances computed by means of similarity matrices, as generators of intrinsic ordering among quantum multimolecular polyhedra

Advanced Review
Ramon Carbó‐Dorca, Diego Barragán
Published Online: Aug 28 2015
DOI:10.1002/wcms.1223

Abstract Full article on Wiley Online Library:   HTML | PDF
Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening

Advanced Review
Qurrat Ul Ain, Antoniya Aleksandrova, Florian D. Roessler, Pedro J. Ballester
Published Online: Aug 28 2015
DOI:10.1002/wcms.1225

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
The topology of fullerenes

Focus Article
Peter Schwerdtfeger, Lukas N Wirz, James Avery
Published Online: Oct 27 2014
DOI:10.1002/wcms.1207

Abstract Full article on Wiley Online Library:   HTML | PDF
Protein–ligand interaction databases: advanced tools to mine activity data and interactions on a structural level

Advanced Review
Therese Inhester, Matthias Rarey
Published Online: Jul 21 2014
DOI:10.1002/wcms.1192

Abstract Full article on Wiley Online Library:   HTML | PDF
Modern 2D QSAR for drug discovery

Advanced Review
Richard A. Lewis, David Wood
Published Online: Apr 25 2014
DOI:10.1002/wcms.1187

Abstract Full article on Wiley Online Library:   HTML | PDF
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