Literature DB >> 27631126

Open source molecular modeling.

Somayeh Pirhadi1, Jocelyn Sunseri2, David Ryan Koes3.   

Abstract

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.
Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Cheminformatics; Molecular modeling; Open source; Software

Mesh：

Substances：

Year:  2016        PMID： 27631126      PMCID： PMC5037051          DOI： 10.1016/j.jmgm.2016.07.008

Source DB:  PubMed          Journal:  J Mol Graph Model        ISSN： 1093-3263            Impact factor:   2.518


  150 in total

1.  ParaDockS: a framework for molecular docking with population-based metaheuristics.

Authors:  René Meier; Martin Pippel; Frank Brandt; Wolfgang Sippl; Carsten Baldauf
Journal:  J Chem Inf Model       Date:  2010-05-24       Impact factor: 4.956

2.  Gabedit--a graphical user interface for computational chemistry softwares.

Authors:  Abdul-Rahman Allouche
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

3.  Efficient Generalized Born Models for Monte Carlo Simulations.

Authors:  Julien Michel; Richard D Taylor; Jonathan W Essex
Journal:  J Chem Theory Comput       Date:  2006-05       Impact factor: 6.006

4.  Projector augmented-wave method.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1994-12-15

5.  SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projects.

Authors:  Paolo Tosco; Thomas Balle; Fereshteh Shiri
Journal:  J Mol Model       Date:  2011-05-15       Impact factor: 1.810

6.  AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

Authors:  Nina Jeliazkova; Vedrin Jeliazkov
Journal:  J Cheminform       Date:  2011-05-16       Impact factor: 5.514

7.  AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.

Authors:  Jacob D Durrant; Steffen Lindert; J Andrew McCammon
Journal:  J Mol Graph Model       Date:  2013-05-23       Impact factor: 2.518

8.  AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment.

Authors:  Jonna C Stålring; Lars A Carlsson; Pedro Almeida; Scott Boyer
Journal:  J Cheminform       Date:  2011-07-28       Impact factor: 5.514

9.  NNScore 2.0: a neural-network receptor-ligand scoring function.

Authors:  Jacob D Durrant; J Andrew McCammon
Journal:  J Chem Inf Model       Date:  2011-11-03       Impact factor: 4.956

10.  A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening.

Authors:  Francois Berenger; Arnout Voet; Xiao Yin Lee; Kam Yj Zhang
Journal:  J Cheminform       Date:  2014-05-10       Impact factor: 5.514
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  16 in total

1.  NGL viewer: web-based molecular graphics for large complexes.

Authors:  Alexander S Rose; Anthony R Bradley; Yana Valasatava; Jose M Duarte; Andreas Prlic; Peter W Rose
Journal:  Bioinformatics       Date:  2018-11-01       Impact factor: 6.937

2.  Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer.

Authors:  Aidin R Balo; Merry Wang; Oliver P Ernst
Journal:  Nat Methods       Date:  2017-11-30       Impact factor: 28.547

3.  Deep learning of pharmacogenomics resources: moving towards precision oncology.

Authors:  Yu-Chiao Chiu; Hung-I Harry Chen; Aparna Gorthi; Milad Mostavi; Siyuan Zheng; Yufei Huang; Yidong Chen
Journal:  Brief Bioinform       Date:  2020-12-01       Impact factor: 11.622

4.  Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.

Authors:  Ngan Nguyen; Ondrej Strnad; Tobias Klein; Deng Luo; Ruwayda Alharbi; Peter Wonka; Martina Maritan; Peter Mindek; Ludovic Autin; David S Goodsell; Ivan Viola
Journal:  IEEE Trans Vis Comput Graph       Date:  2021-01-28       Impact factor: 4.579

5.  Web3DMol: interactive protein structure visualization based on WebGL.

Authors:  Maoxiang Shi; Juntao Gao; Michael Q Zhang
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

6.  Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

Authors:  Pierre Tremouilhac; An Nguyen; Yu-Chieh Huang; Serhii Kotov; Dominic Sebastian Lütjohann; Florian Hübsch; Nicole Jung; Stefan Bräse
Journal:  J Cheminform       Date:  2017-09-25       Impact factor: 5.514

7.  The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

Authors:  Peter W Rose; Andreas Prlić; Ali Altunkaya; Chunxiao Bi; Anthony R Bradley; Cole H Christie; Luigi Di Costanzo; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Rachel Kramer Green; David S Goodsell; Brian Hudson; Tara Kalro; Robert Lowe; Ezra Peisach; Christopher Randle; Alexander S Rose; Chenghua Shao; Yi-Ping Tao; Yana Valasatava; Maria Voigt; John D Westbrook; Jesse Woo; Huangwang Yang; Jasmine Y Young; Christine Zardecki; Helen M Berman; Stephen K Burley
Journal:  Nucleic Acids Res       Date:  2016-10-27       Impact factor: 16.971

8.  A simple open source bioinformatic methodology for initial exploration of GPCR ligands' agonistic/antagonistic properties.

Authors:  Athanasios A Panagiotopoulos; Christina Papachristofi; Konstantina Kalyvianaki; Panagiotis Malamos; Panayiotis A Theodoropoulos; George Notas; Theodora Calogeropoulou; Elias Castanas; Marilena Kampa
Journal:  Pharmacol Res Perspect       Date:  2020-08

9.  Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies.

Authors:  Dmitry Suplatov; Yana Sharapova; Elizaveta Geraseva; Vytas Švedas
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

10.  ProteinsPlus: interactive analysis of protein-ligand binding interfaces.

Authors:  Katrin Schöning-Stierand; Konrad Diedrich; Rainer Fährrolfes; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Ruben Steinegger; Matthias Rarey
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971
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