Open source molecular modeling.

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.

[1]  David S. Goodsell,et al.  A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..

[2]  Kwong-Sak Leung,et al.  Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets , 2015, Molecular informatics.

[3]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[4]  Michael Schroeder,et al.  PLIP: fully automated protein–ligand interaction profiler , 2015, Nucleic Acids Res..

[5]  J. Sussman,et al.  JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia , 2013 .

[6]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[7]  Tao Jiang,et al.  ChemmineR: a compound mining framework for R , 2008, Bioinform..

[8]  Thorsten Meinl,et al.  KNIME-CDK: Workflow-driven cheminformatics , 2013, BMC Bioinformatics.

[9]  Andreas Hofmann,et al.  A practical Java tool for small-molecule compound appraisal , 2015, Journal of Cheminformatics.

[10]  Xiaohua Zhang,et al.  Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines , 2013, J. Comput. Chem..

[11]  Jesús A. Izaguirre,et al.  MDLab: A molecular dynamics simulation prototyping environment , 2009, J. Comput. Chem..

[12]  Clarke W. Earley.  CH5M3D: an HTML5 program for creating 3D molecular structures , 2013, Journal of Cheminformatics.

[13]  Nina Jeliazkova,et al.  AMBIT RESTful web services: an implementation of the OpenTox application programming interface , 2011, J. Cheminformatics.

[14]  Nina Jeliazkova,et al.  Ambit‐Tautomer: An Open Source Tool for Tautomer Generation , 2013, Molecular informatics.

[15]  Vijay S. Pande,et al.  PAPER—Accelerating parallel evaluations of ROCS , 2010, J. Comput. Chem..

[16]  Toni Giorgino,et al.  MEMBPLUGIN: studying membrane complexity in VMD , 2014, Bioinform..

[17]  David E. Gloriam,et al.  The contribution of atom accessibility to site of metabolism models for cytochromes P450. , 2013, Molecular pharmaceutics.

[18]  Frank Noé,et al.  PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. , 2015, Journal of chemical theory and computation.

[19]  Abdul-Rahman Allouche,et al.  Gabedit—A graphical user interface for computational chemistry softwares , 2011, J. Comput. Chem..

[20]  Ignacio Ponzoni,et al.  Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods , 2015, Journal of Cheminformatics.

[21]  Piotr Zielenkiewicz,et al.  Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field , 2015, Journal of Cheminformatics.

[22]  Rommie E. Amaro,et al.  POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics , 2014, Journal of chemical theory and computation.

[23]  Konrad Hinsen,et al.  The molecular modeling toolkit: A new approach to molecular simulations , 2000, J. Comput. Chem..

[24]  Gert Thijs,et al.  Pharao: pharmacophore alignment and optimization. , 2008, Journal of molecular graphics & modelling.

[25]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[26]  Dan Ventura,et al.  Rubabel: wrapping open Babel with Ruby , 2013, Journal of Cheminformatics.

[27]  Nicola Zonta,et al.  Accessible haptic technology for drug design applications , 2009, Journal of molecular modeling.

[28]  Ivet Bahar,et al.  ProDy: Protein Dynamics Inferred from Theory and Experiments , 2011, Bioinform..

[29]  Jacob D. Durrant,et al.  NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function , 2011, J. Chem. Inf. Model..

[30]  Nicholas B Rego,et al.  3Dmol.js: molecular visualization with WebGL , 2014, Bioinform..

[31]  Hans-Peter Lenhof,et al.  BALLView: a tool for research and education in molecular modeling , 2006, Bioinform..

[32]  Thomas Sander,et al.  DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis , 2015, J. Chem. Inf. Model..

[33]  Paolo Cignoni,et al.  Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization , 2006, IEEE Transactions on Visualization and Computer Graphics.

[34]  Ferran Sanz,et al.  eTOXlab, an open source modeling framework for implementing predictive models in production environments , 2015, Journal of Cheminformatics.

[35]  Semen O. Yesylevskyy,et al.  Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python , 2015, J. Comput. Chem..

[36]  Tom L. Blundell,et al.  USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints , 2012, Journal of Cheminformatics.

[37]  Maik Moeller,et al.  An Introduction To Chemoinformatics , 2016 .

[38]  Melanie C. Burger,et al.  ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics , 2015, Journal of Cheminformatics.

[39]  J. Daniel Gezelter.  Open Source and Open Data Should Be Standard Practices. , 2015, The journal of physical chemistry letters.

[40]  Xavier Barril,et al.  rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids , 2014, PLoS Comput. Biol..

[41]  Stefan Kramer,et al.  CheS-Mapper - Chemical Space Mapping and Visualization in 3D , 2012, Journal of Cheminformatics.

[42]  Pierre Baldi,et al.  Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules , 2013, J. Chem. Inf. Model..

[43]  Marco Biasini,et al.  pv: v1.8.1 , 2015 .

[44]  Axel Drefahl,et al.  CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures , 2011, J. Cheminformatics.

[45]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[46]  José Xavier-Neto,et al.  KVFinder: steered identification of protein cavities as a PyMOL plugin , 2014, BMC Bioinformatics.

[47]  Piotr Cieplak,et al.  The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. , 2010, Physical chemistry chemical physics : PCCP.

[48]  Peter Pulay,et al.  What Is the Price of Open-Source Software? , 2015, The journal of physical chemistry letters.

[49]  Andreas Zell,et al.  Probabilistic Modeling of Conformational Space for 3D Machine Learning Approaches , 2010, Molecular informatics.

[50]  R J Bartlett,et al.  Parallel implementation of electronic structure energy, gradient, and Hessian calculations. , 2008, The Journal of chemical physics.

[51]  Joost VandeVondele,et al.  cp2k: atomistic simulations of condensed matter systems , 2014 .

[52]  Stefano de Gironcoli,et al.  QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[53]  Rajarshi Guha,et al.  Chemical Informatics Functionality in R , 2007 .

[54]  CHUN WEI YAP,et al.  PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints , 2011, J. Comput. Chem..

[56]  Egon L. Willighagen,et al.  The Blue Obelisk—Interoperability in Chemical Informatics , 2006, J. Chem. Inf. Model..

[57]  Leonid A. Bulavin,et al.  JANPA: An open source cross-platform implementation of the Natural Population Analysis on the Java platform , 2014 .

[58]  Jan H. Jensen,et al.  FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations , 2012, PloS one.

[59]  Thierry Matthey,et al.  ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics , 2004, TOMS.

[60]  Matthew L. Leininger,et al.  Psi4: an open‐source ab initio electronic structure program , 2012 .

[61]  Brett M. Bode,et al.  MacMolPlt: a graphical user interface for GAMESS. , 1998, Journal of molecular graphics & modelling.

[62]  Kevin Lawson,et al.  LICSS - a chemical spreadsheet in microsoft excel , 2012, Journal of Cheminformatics.

[63]  J Andrew McCammon,et al.  AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. , 2013, Journal of molecular graphics & modelling.

[64]  F. Javier Luque,et al.  MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories , 2011, Bioinform..

[65]  David M. Ceperley,et al.  Quantum Monte Carlo algorithms: making most of large-scale multi/many-core clusters , 2010 .

[66]  Richard J. Hanson,et al.  J‐ICE: a new Jmol interface for handling and visualizing crystallographic and electronic properties , 2011 .

[67]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[68]  Marco De Vivo.  Bridging quantum mechanics and structure-based drug design. , 2011, Frontiers in bioscience.

[69]  Ian A. Watson,et al.  Rules for identifying potentially reactive or promiscuous compounds. , 2012, Journal of medicinal chemistry.

[70]  Vincent Le Guilloux,et al.  Mining collections of compounds with Screening Assistant 2 , 2012, Journal of Cheminformatics.

[71]  P. M. Rodger,et al.  DL_POLY: Application to molecular simulation , 2002 .

[72]  Thomas J Lane,et al.  MDTraj: a modern, open library for the analysis of molecular dynamics trajectories , 2014, bioRxiv.

[73]  Stefan Goedecker,et al.  Accurate and efficient linear scaling DFT calculations with universal applicability. , 2015, Physical chemistry chemical physics : PCCP.

[74]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[75]  Yan Wang,et al.  fmcsR: mismatch tolerant maximum common substructure searching in R , 2013, Bioinform..

[76]  Thorsten Meinl,et al.  KNIME - the Konstanz information miner: version 2.0 and beyond , 2009, SKDD.

[77]  Igor V. Filippov,et al.  Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution , 2009, J. Chem. Inf. Model..

[78]  Shirley Moore,et al.  Scaling the RMG quantum mechanics code , 2012 .

[79]  David E. Gloriam,et al.  SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism. , 2010, ACS medicinal chemistry letters.

[80]  Jacob D. Durrant,et al.  AutoClickChem: Click Chemistry in Silico , 2012, PLoS Comput. Biol..

[81]  Adrià Cereto-Massagué,et al.  The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites , 2013, Journal of Cheminformatics.

[82]  Goran Kovacevic,et al.  Luscus: molecular viewer and editor for MOLCAS , 2015, Journal of Cheminformatics.

[83]  Alan Grossfield,et al.  Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations , 2014, J. Comput. Chem..

[84]  Thorsten Meinl,et al.  KNIME: The Konstanz Information Miner , 2007, GfKl.

[85]  Kam Y. J. Zhang,et al.  A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening , 2014, Journal of Cheminformatics.

[86]  Eric K. Brefo-Mensah,et al.  mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code , 2012, Journal of Cheminformatics.

[87]  Piotr Zielenkiewicz,et al.  DiSCuS: An Open Platform for (Not Only) Virtual Screening Results Management , 2014, J. Chem. Inf. Model..

[88]  Christoph R Jacob.  How Open Is Commercial Scientific Software? , 2016, The journal of physical chemistry letters.

[89]  Egon L. Willighagen,et al.  CDK-Taverna: an open workflow environment for cheminformatics , 2010, BMC Bioinformatics.

[90]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[91]  Scott Boyer,et al.  AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment , 2011, J. Cheminformatics.

[92]  Rui M. V. Abreu,et al.  MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters , 2010, J. Cheminformatics.

[93]  Eugene I Shakhnovich,et al.  OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. , 2016, Journal of medicinal chemistry.

[94]  Ségolène Caboche.  LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions , 2013, Journal of Cheminformatics.

[95]  Reed B. Jacob,et al.  DockoMatic 2.0: High Throughput Inverse Virtual Screening and Homology Modeling , 2013, J. Chem. Inf. Model..

[96]  Manish Sud,et al.  MayaChemTools: An Open Source Package for Computational Drug Discovery , 2016, J. Chem. Inf. Model..

[97]  Andreas Vitalis,et al.  Methods for Monte Carlo simulations of biomacromolecules. , 2009, Annual reports in computational chemistry.

[98]  Miguel A. L. Marques,et al.  Libxc: A library of exchange and correlation functionals for density functional theory , 2012, Comput. Phys. Commun..

[99]  M. Biasini,et al.  OpenStructure: an integrated software framework for computational structural biology , 2013, Acta crystallographica. Section D, Biological crystallography.

[100]  Christoph Steinbeck,et al.  JChemPaint - Using the collaborative forces of the Internet to develop a free editor for 2D chemical structures , 2000 .

[101]  Diwakar Shukla,et al.  OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. , 2013, Journal of chemical theory and computation.

[102]  David Ryan Koes,et al.  Pharmer: Efficient and Exact Pharmacophore Search , 2011, J. Chem. Inf. Model..

[103]  Garland R. Marshall,et al.  An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design , 2016, J. Chem. Inf. Model..

[104]  John B. O. Mitchell,et al.  A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking , 2010, Bioinform..

[105]  Christian Borgelt,et al.  MoSS: a program for molecular substructure mining , 2005 .

[106]  Deacon John Sweeney.  A Computational Tool for Biomolecular Structure Analysis Based On Chemical and Enzymatic Modification of Native Proteins , 2011 .

[107]  Emanuel H. Rubensson,et al.  Kohn-Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage. , 2011, Journal of chemical theory and computation.

[108]  Jonas Boström,et al.  Molecular Rift: Virtual Reality for Drug Designers , 2015, J. Chem. Inf. Model..

[109]  Blöchl,et al.  Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.

[110]  Rajarshi Guha,et al.  Synergy Maps: exploring compound combinations using network-based visualization , 2015, Journal of Cheminformatics.

[111]  H WittenIan,et al.  The WEKA data mining software , 2009 .

[112]  René Meier,et al.  ParaDockS: A Framework for Molecular Docking with Population-Based Metaheuristics , 2010, J. Chem. Inf. Model..

[113]  Christoph Steinbeck,et al.  OrChem - An open source chemistry search engine for Oracle® , 2009, J. Cheminformatics.

[114]  Andrew Dalke.  chemfp - fast and portable fingerprint formats and tools , 2011, J. Cheminformatics.

[115]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[116]  Alexander S. Rose,et al.  NGL Viewer: a web application for molecular visualization , 2015, Nucleic Acids Res..

[117]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[118]  Xavier Andrade,et al.  Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems. , 2015, Physical chemistry chemical physics : PCCP.

[119]  José Mario Martínez,et al.  PACKMOL: A package for building initial configurations for molecular dynamics simulations , 2009, J. Comput. Chem..

[120]  Alexander P. Lyubartsev,et al.  M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures , 2000 .

[121]  Stefan Goedecker,et al.  Daubechies wavelets for linear scaling density functional theory. , 2014, The Journal of chemical physics.

[122]  C. Steinbeck,et al.  Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. , 2006, Current pharmaceutical design.

[123]  Stefan Goedecker,et al.  ABINIT: First-principles approach to material and nanosystem properties , 2009, Comput. Phys. Commun..

[124]  Olivier Sperandio,et al.  One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. , 2013, Drug discovery today.

[125]  Martin Mozina,et al.  Orange: data mining toolbox in python , 2013, J. Mach. Learn. Res..

[126]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[127]  Oliver Beckstein,et al.  MDAnalysis: A toolkit for the analysis of molecular dynamics simulations , 2011, J. Comput. Chem..

[128]  Lars Carlsson,et al.  Stereo Signature Molecular Descriptor , 2013, J. Chem. Inf. Model..

[129]  Pierre Tufféry,et al.  Frog2: Efficient 3D conformation ensemble generator for small compounds , 2010, Nucleic Acids Res..

[130]  Charlotte M. Deane,et al.  Freely Available Conformer Generation Methods: How Good Are They? , 2012, J. Chem. Inf. Model..

[131]  Michael Grüninger,et al.  Introduction , 2002, CACM.

[132]  David Ryan Koes,et al.  Pharmit: interactive exploration of chemical space , 2016, Nucleic Acids Res..

[133]  Paolo Tosco,et al.  SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projects , 2011, Journal of molecular modeling.

[134]  Jeremy C. Smith,et al.  VinaMPI: Facilitating multiple receptor high‐throughput virtual docking on high‐performance computers , 2013, J. Comput. Chem..

[135]  David Ryan Koes,et al.  Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise , 2013, J. Chem. Inf. Model..

[136]  Ross C. Walker,et al.  An overview of the Amber biomolecular simulation package , 2013 .

[137]  Reinhold Schneider,et al.  Daubechies wavelets as a basis set for density functional pseudopotential calculations. , 2008, The Journal of chemical physics.

[138]  Noel M. O'Boyle,et al.  Cinfony – combining Open Source cheminformatics toolkits behind a common interface , 2008, Chemistry Central journal.

[139]  Xavier Assfeld,et al.  New Insight into the Topology of Excited States through Detachment/Attachment Density Matrices-Based Centroids of Charge. , 2014, Journal of chemical theory and computation.

[140]  Sabine C. Mueller,et al.  BALL - biochemical algorithms library 1.3 , 2010, BMC Bioinformatics.

[141]  Keijo Hämäläinen,et al.  ERKALE—A flexible program package for X‐ray properties of atoms and molecules , 2012, J. Comput. Chem..

[142]  Karsten W. Jacobsen,et al.  An object-oriented scripting interface to a legacy electronic structure code , 2002, Comput. Sci. Eng..

[143]  Michal Brylinski,et al.  eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands , 2013, Journal of Computer-Aided Molecular Design.

[144]  Paul Tavan,et al.  Optimizing the Accuracy and Efficiency of Fast Hierarchical Multipole Expansions for MD Simulations. , 2012, Journal of chemical theory and computation.

[145]  Stefan Kramer,et al.  CheS-Mapper 2.0 for visual validation of (Q)SAR models , 2014, Journal of Cheminformatics.

[146]  Tjerk P. Straatsma,et al.  NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations , 2010, Comput. Phys. Commun..

[147]  Carsten Baldauf,et al.  First-Principles Molecular Structure Search with a Genetic Algorithm , 2015, J. Chem. Inf. Model..

[148]  Norbert Haider,et al.  Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach , 2010, Molecules.

[149]  Javier Setoain,et al.  MEPSA: minimum energy pathway analysis for energy landscapes , 2015, Bioinform..

[150]  N. A. Romero,et al.  Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[151]  Chris Morley,et al.  Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit , 2008, Chemistry Central journal.

[152]  Noel M. O'Boyle,et al.  cclib: A library for package‐independent computational chemistry algorithms , 2008, J. Comput. Chem..

[153]  G. Patlewicz,et al.  An evaluation of the implementation of the Cramer classification scheme in the Toxtree software , 2008, SAR and QSAR in environmental research.

[154]  Daniel Svozil,et al.  Molpher: a software framework for systematic chemical space exploration , 2014, Journal of Cheminformatics.

[155]  Mohamad Mohebifar,et al.  Chemozart: a web-based 3D molecular structure editor and visualizer platform , 2015, Journal of Cheminformatics.

[156]  Stefan Wetzel,et al.  Interactive exploration of chemical space with Scaffold Hunter. , 2009, Nature chemical biology.

[157]  Kwong-Sak Leung,et al.  idock: A multithreaded virtual screening tool for flexible ligand docking , 2012, 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

[158]  Luc Patiny,et al.  Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia , 2015, Journal of Cheminformatics.

[159]  Christian Janssen,et al.  Object-Oriented Implementation of Parallel Ab Initio Programs , 1995 .

[160]  Carole A. Goble,et al.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud , 2013, Nucleic Acids Res..

[161]  Alexander D. MacKerell,et al.  Robustness in the fitting of molecular mechanics parameters , 2015, J. Comput. Chem..

[162]  Jean-Loup Faulon,et al.  OMG: Open Molecule Generator , 2012, Journal of Cheminformatics.

[163]  Isidro Cortes-Ciriano,et al.  Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets , 2016, Journal of Cheminformatics.

[164]  Adrià Cereto-Massagué,et al.  DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets , 2012, Bioinform..

[165]  Peter Murray-Rust,et al.  Chemical Name to Structure: OPSIN, an Open Source Solution , 2011, J. Chem. Inf. Model..

[166]  Anita R. Maguire,et al.  Confab - Systematic generation of diverse low-energy conformers , 2011, J. Cheminformatics.

[167]  G. Schneider,et al.  PocketPicker: analysis of ligand binding-sites with shape descriptors , 2007, Chemistry Central Journal.

[168]  Hans-Christian Hege,et al.  ORBKIT: A modular python toolbox for cross‐platform postprocessing of quantum chemical wavefunction data , 2016, J. Comput. Chem..

[169]  Peter Ertl,et al.  JSME: a free molecule editor in JavaScript , 2013, Journal of Cheminformatics.

[170]  G. Ullmann,et al.  McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm , 2010, Journal of molecular modeling.

[171]  Arthur J Olson,et al.  Small-molecule library screening by docking with PyRx. , 2015, Methods in molecular biology.

[172]  Taisuke Ozaki,et al.  Efficient projector expansion for the ab initio LCAO method , 2005 .

[173]  Alexey Savelyev,et al.  Indigo: universal cheminformatics API , 2011, J. Cheminformatics.

[174]  Egon L. Willighagen,et al.  Bioclipse 2: A scriptable integration platform for the life sciences , 2009, BMC Bioinformatics.

[175]  I. Bahar,et al.  Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. , 2013, Journal of chemical theory and computation.

[176]  Rainer Schrader,et al.  Small Molecule Subgraph Detector (SMSD) toolkit , 2009, J. Cheminformatics.

[177]  Massimiliano Bonomi,et al.  PLUMED 2: New feathers for an old bird , 2013, Comput. Phys. Commun..

[178]  Paolo Tosco,et al.  Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields , 2011, Journal of molecular modeling.

[179]  Igor V. Filippov,et al.  Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on , 2011, J. Cheminformatics.

[180]  Hong Liu,et al.  GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit , 2013, J. Comput. Chem..

[181]  G. Kresse,et al.  From ultrasoft pseudopotentials to the projector augmented-wave method , 1999 .

[182]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[183]  Gerhard Klebe,et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations , 2007, Nucleic Acids Res..

[184]  Joshua L Adelman,et al.  WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis. , 2015, Journal of chemical theory and computation.

[185]  Thomas J Lane,et al.  MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. , 2011, Journal of chemical theory and computation.

[186]  Laurence Miguet,et al.  Shape: automatic conformation prediction of carbohydrates using a genetic algorithm , 2009, J. Cheminformatics.

[187]  Robert M. Hanson,et al.  Jmol – a paradigm shift in crystallographic visualization , 2010 .

[188]  Jaques Reifman,et al.  DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0 , 2008, Chemistry Central journal.

[189]  Isidro Cortes-Ciriano,et al.  Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules , 2015, Journal of Cheminformatics.

[190]  Julien Michel,et al.  Efficient Generalized Born Models for Monte Carlo Simulations. , 2006, Journal of chemical theory and computation.

[191]  Stefan Höck,et al.  chemf: A purely functional chemistry toolkit , 2012, Journal of Cheminformatics.

[192]  Jonathan D. Hirst,et al.  TMACC: Interpretable Correlation Descriptors for Quantitative Structure-Activity Relationships , 2007, J. Chem. Inf. Model..