Open source molecular modeling

scientific article

Open source molecular modeling is …
instance of (P31):
scholarly articleQ13442814
review articleQ7318358

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P356DOI10.1016/J.JMGM.2016.07.008
P932PMC publication ID5037051
P698PubMed publication ID27631126

P50authorSomayeh PirhadiQ84973093
Jocelyn SunseriQ88259734
P2093author name stringDavid Ryan Koes
P2860cites workGalaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesQ21092859
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A machine learning approach to predicting protein-ligand binding affinity with applications to molecular dockingQ28276262
BALLView: a tool for research and education in molecular modelingQ28285390
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloudQ28290043
AutoClickChem: click chemistry in silicoQ28481518
FragIt: a tool to prepare input files for fragment based quantum chemical calculationsQ28483844
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acidsQ28537716
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PocketPicker: analysis of ligand binding-sites with shape descriptors.Q30364721
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Accurate and efficient linear scaling DFT calculations with universal applicability.Q50917667
Freely available conformer generation methods: how good are they?Q51386173
Ambient occlusion and edge cueing to enhance real time molecular visualization.Q51628730
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chemfp - fast and portable fingerprint formats and toolsQ59265935
Indigo: universal cheminformatics APIQ59265960
How Open Is Commercial Scientific Software?Q62099141
ERKALE-A flexible program package for X-ray properties of atoms and moleculesQ83974967
SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projectsQ84107239
Functionality pattern matching as an efficient complementary structure/reaction search tool: an open-source approachQ84748533
New Insight into the Topology of Excited States through Detachment/Attachment Density Matrices-Based Centroids of ChargeQ86749971
Daubechies wavelets for linear scaling density functional theoryQ87989941
DataWarrior: an open-source program for chemistry aware data visualization and analysisQ30882770
Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data SetsQ31119539
Pybel: a Python wrapper for the OpenBabel cheminformatics toolkitQ33323081
ChemmineR: a compound mining framework for R.Q33348428
Interactive exploration of chemical space with Scaffold HunterQ33475598
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The R.E.D. tools: advances in RESP and ESP charge derivation and force field library buildingQ33614754
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Methods for Monte Carlo simulations of biomacromoleculesQ33813152
ProDy: protein dynamics inferred from theory and experimentsQ33864431
MDAnalysis: a toolkit for the analysis of molecular dynamics simulationsQ33875319
Pharmer: efficient and exact pharmacophore searchQ33909006
Optical structure recognition software to recover chemical information: OSRA, an open source solutionQ33926888
Frog2: Efficient 3D conformation ensemble generator for small compounds.Q33957419
NNScore 2.0: a neural-network receptor-ligand scoring functionQ34053706
AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environmentQ34204323
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.Q34249296
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.Q34331455
Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like moleculesQ34353087
fmcsR: mismatch tolerant maximum common substructure searching in R.Q34365383
mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X codeQ34432421
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraintsQ34468310
NGL Viewer: a web application for molecular visualizationQ34474309
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume CharacteristicsQ34503061
An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design.Q34505706
Mining collections of compounds with Screening Assistant 2Q34552776
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.Q34560447
VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers.Q34787480
Rubabel: wrapping open Babel with RubyQ34863575
CH5M3D: an HTML5 program for creating 3D molecular structuresQ35045807
Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.Q35346073
3Dmol.js: molecular visualization with WebGL.Q35367250
Small-molecule library screening by docking with PyRxQ35548740
P407language of work or nameEnglishQ1860
P921main subjectfree and open-source softwareQ506883
open-source softwareQ1130645
P304page(s)127-143
P577publication date2016-09-01
P1433published inJournal of Molecular Graphics & ModellingQ3186928
P1476titleOpen source molecular modeling
P478volume69

Reverse relations

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