World Index of BioMolecular Visualization Resources
Commerical Software for Molecular Visualization and Modeling
Titles
Subjects
Authors:
Detailed
Compact
HOME
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Accelrys, Inc. (formerly MSI)
(www.accelrys.com
)
- Insight II
- QUANTA Environment
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Audie, Joseph
(www.cmdbioscience.com
)
- CMD Bioscience
Description
(Cross-indexing terms:
scoring function; drug design; free energy; docking; protein-protein)
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Baum, Daniel
(www.amiravis.com
)
- AmiraMol
Description
(Cross-indexing terms:
Molecular Visualization; Molecular Surface; Alignment)
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Berndt, Michael
(www.crystalimpact.com
)
- Diamond - Visual Crystal Structure Information System
Description
(Cross-indexing terms:
crystal structure; inorganics; minerals; surfaces; proteins; coordination polyhedra; thermal ellipsoids; VRML)
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Bladon, Peter
(www.interprobe.co.uk
)
- INTERCHEM system
Description
(Cross-indexing terms:
Molecular modelling; biolmolecules; molecular mechanics; SMILES)
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Bonner, Thomas
(www.geocities.com
)
- Apollonius
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ChemAxon, Ltd
(www.chemaxon.com
)
- Marvin Applets and JavaBeans
Description
(Cross-indexing terms:
applet; JavaBeans; Java; chemical database; Windows; Unix; Mac; IE; Netscape; Mozilla; Molfile; SDfile; RDfile; Rgfile; Rxnfile; SMILES; SMARTS; XYZ; PDB; CML; JPG; PNG; SVG; POV-Ray; stereochemistry; query atoms; query bonds; R-groups; R-logic; reaction; atom-mapping; 2D; 3D; wireframe; sticks; ball-and-stick; clean; animation; table of structures; reactions; E/Z double bonds; R/S chirality; ABS/OR/AND enhanced stereo; query stereo configuration; prediction; plugin; pKa; logP; logD; polar surface area (PSA); charge distribution; polarizability prediction; H-bond aceptor/donor; major microspecies; reactivity; refractivity; elemental analysis; topology analysis)
- Screen
Description
(Cross-indexing terms:
virtual screening; molecular descriptors; fingerprint; pharmacophores; java; chemical database; focused library; scaling-fingerprint; scaffold hopping; topological fingerprint; topological cross-correlation histogram; enrichment; drug discovery)
- Reactor
Description
(Cross-indexing terms:
virtual synthesis; reaction engine; combinatorial chemistry; JChem; chemically feasible; multi-step)
- JChem Base and JChem Cartridge
Description
(Cross-indexing terms:
structure search; non structural data; exact; substructure; similarity; reaction; search; database; Oracle; cartridge; Marvin; API; 2D hashed fingerprint, pharmacophore, chemical; fingerprint; SQL; Access; MySQL; API; Java; SMARTS; R-Group; Chemical Terms; query; pharmacophore fingerprint)
- Calculator Plugins
Description
(Cross-indexing terms:
pKa; logP; logD; polar surface area (PSA); charge distribution; polarizability predictions; java; plugin; Marvin; JChem; prediction; octanol/water partition coefficient; QSAR; ionization equilibrium; apparent logP; hydrophobicity; molecular mass; exact mass; chemical formula; elemental composition (w/w%); drug discovery; Huckel Analysis; Hydrogen Bond Donor; Hydrogen Bond Acceptor; Major Microspecies; Refractivity; Structure Topology; rotatable bond; ADME; ADMETOX)
- Fragmenter
Description
(Cross-indexing terms:
fragmenter; cleave; reaction; molecule; algorithm; RECAP; drug; design; virtual; synthesis)
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Doherty, David
(www.bitwixt.com
)
- The Atomsmith Molecular Exploration Kit
Description
(Cross-indexing terms:
molecular modeling; educational sofware; model building; molecular visualization)
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Gunda, Tamas
(web.interware.hu
)
- Mol2Mol converts, manipulates and displays various molecule files
Description
(Cross-indexing terms:
conversion between atomic coordinate file formats; PDB subformats; molecule files; calculation of geometrical data; POVRAY)
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Gunda, Tamas E.
(dragon.klte.hu
)
- Comparison of Five Chemical Drawing Programs
Description
(English, Hungarian)
(Cross-indexing terms:
drawing software, chemical; comparison of chemical drawing software; review of chemical drawing software)
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Jones, Alwyn
(xray.bmc.uu.se
)
- O
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Karplus, Martin
(www.accelrys.com
)
- CHARMm
Description
(Cross-indexing terms:
modeling, protein; dynamics, molecular; mechanics, molecular)
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Kraulis, Per
(www.avatar.se
)
- MolScript
Description
(Cross-indexing terms:
Publication-quality images)
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Muscat, Andre
(www.kalsaya.com
)
- KVizPro
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Nikitin, Alexey
(www.agilemolecule.com
)
- Ascalaph
Description
(Cross-indexing terms:
modeling, molecular; design, molecular; construction, molecular; mechanic; dynamic; builder; simulation; quantum)
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OpenEye Scientific Software, Inc
(www.eyesopen.com
)
- VIDA
Description
(Cross-indexing terms:
python; publication-quality images; spreadsheet; 2D; Windows; Mac; Unix; Linux; OpenEye)
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Palmer, David
(www.crystalmaker.com
)
- CrystalMaker: Crystal and molecular structures visualization and diffraction simulation, for Mac and Windows
Description
(Cross-indexing terms:
CrystalDiffract; SingleCrystal; crystal structures visualization software; diffraction simulation; TEM diffraction; x-ray powder diffraction; stereographic projections)
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patrick ,Urbaniak
(pro.chemist.online.fr
)
- ProChemist
Description
(Cross-indexing terms:
modeling software; QSAR; pKa calculation)
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Surles, Mark, et al.
(www.mdl.com
)
- Sculpt
Description
(Cross-indexing terms:
molecular mechanics; mechanics, molecular; MDL; Interactive Simulations, formerly, now MDL)
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Thiessen, Paul
(www.ChemicalGraphics.com
)
- PovChem
Description
(Cross-indexing terms:
povchem; raytracer; publication-quality images; services)
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Tripos, Inc.
(www.tripos.com
)
- SYBYL
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Vriend, Gert
(www.cmbi.kun.nl
)
- WHAT IF
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Zhorov, Boris
(www.zmmsoft.com
)
- ZMM - An Internal Coordinate Molecular Modeling Program
Description
(Cross-indexing terms:
protein; nucleic acid; drug design; inhibitor design; ion channel; antifreeze proteins; enzymes; protease; internal coordinate molecular mechanics; Monte Carlo minimization.)
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Zsoldos, Zsolt
(simbiosys.ca
)
- SPROUT
Description
(Cross-indexing terms:
drug design; publication-quality images; modeling)
24 total first authors.
Visitor-Maintained Index
programming by Trevor D. Kramer.