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For unlisted software, try SoftwareSeek. Companies producing software packages spanning several categories
are listed under Computing/Companies.
 
3D Structure Generation
Corina (MN)
ChemFrontier
 
3D-QSAR
GERM
GOLPE
GRID
HASL
hint!
Quasar
  
ADMET Prediction
ADMEWORKS
Amedis
Camitro
iDEA
OraSpotter
PK-Map
PK-Sim
Simulations Plus
  
Bioinformatics
ANTHEPROT
Artemis
BioTools
CE 3
CombAlign
Darwin
Eddy's Lab Tools
Expression
GeneMine
GeneLinker
ICM-Bioinformatics
LOOPP
Orpheus
Pred/Phrap/Consed
PROTARCH
Phylogeny List
Pipeline Pilot
PISCES
Protana
Sanger Centre
Setter
STAMP
ToPLign
  
Biopolymer Tools
DOMPLOT
HBPLUS
LigPlot
naccess
NUCPLOT
PROCHECK
PROCOMP
SCWRL
SURFNET
TOPOFIT
X-SITE
    
Cavity Search
PASS
 
Code
Applied Statistics Algorithms
GAMS
HotGAMS
Numerical Algorithms Group
StatCodes
  
Compound Warehousing
C@ROL
ChemAxon
JChemBase
workaccelerator
  
Computational Chemistry 
ADF
AMPAC
AMSOL
Basis Set Exchange
DivCon
DYNAMO (QM/MM)
DYNAMO (NMR)
ECEPPAK
Gaussian
GAMESS
Harmony
LocalSCF
MCCE
MolPro
MOPAC
MOPAC with MOZYME
NWChem
OpenMol
ParaSurf
PQS
Q-Chem
QCPE
Quantum

Turbo-Frodo
VASP/VAMP
WebMO
YASARA
  
Conformer Generation
Balloon

CONFLEX
Conformer
OMEGA
OMICRON
ROTATE
Xedex
Data Analysis/Modeling 
Analyze/StripMiner
CoPlot
DataFit
DMax Chemistry Assistant
DynaFit
Equbits
Fitter
Feature Trees
FEMLAB
FlexPDE
IGOR Pro
Kinetica
Minitab
Mathematica
MLAB
MAPLE
MATLAB
Miner3D
Neural Network Add-Ins for Excel
NLREG
NONMEM
Origin
PK Solutions
PLS_Toolbox
PopKinetics
PSI-Plot & ProStat
Research Systems
SAAM II
Scientist
SONNIA
S-PLUS
Statistica
STODE
Teranode Design Suite
Unsupervised Forward Selection
Weka
XploRe
 
Data Management/Mining 
CHED
ChemFileBrowser
ChemTK
ChemTree
Clementine
DiscoveryCenter
eLabBook
Filter
GhostMiner
HelixTree
LeadScope
LUCIA
Metabase
NuGenesis SDMS
Pervasive
Personal Chemistry Client
PowerMV
quattro
QCluster
Salford Systems
Recommind
VIDA
 
Data Visualization
MayaVi
  
De Novo Design
BUILDER
CombiBuild
CONCERTS
LigBuilder
MCDNLG
MolGrow
NEWLEAD
RASSE
SMoG
SPROUT
  
Distributed Computing
AVAKI
CSE-Online
Entropia
Models@Home
Platform
Scientific
Turboworx
United Devices
 
Docking/Scoring
3-DPL Map
Affinity
Autodock
CAVEAT
CLIX
Dock
DockIT
DockVision
eHits
ESCHER NG
FlexE
FlexX
FlexX-Pharm
FlexX-Scan
FLOG
FRED
GOLD
GRAMM
Hammerhead
ICM-VLS
PRO_LEADS
RosettaDock
Score
Situs
SenSitus
Slide
VRDD
X-Score (scoring only)
Drawing and Nomenclature
ChemDraw Net Plugin
ChemInnovation
   
Electrostatics
APBS
DelPhi
QUACPAC
ZAP (1, 2

File Conversion
Babel
CLiDE
CLIFF
Open Babel
SciConvert

Kits/Libraries/Toolboxes
CDK
JOELib
OEChem
OELib/Open Babel

 
Link Collections
EBI Biocatalog
GAMS
Mathtools
NBCR Software
Netlib
Network Science List
NIH CMM List
 
Literature Management
JabRef
Librarian
PowerRef
    
MD/MC 
AMBER
BOSS/MCPRO
CHARMM
DL_POLY
CYANA 
EGO
GROMACS
IED
ISIM
MMC
MOIL
MOIL-View
NAMD
nMOLDYN
Q
UHBD
   
Metabolism Prediction
Meta
MetaSite
Meteor
      
Molecular Visualization
AGM View & Build
AstexViewer
B (formerly Biomer)
BALLview
BioBox
BKChem
ChemSymphony
CheVi
Chime Plugin
Chimera
Cn3D
Deep View (Swiss-PDB Viewer)
Dino
Flex
FlexV
Flo
Friend
Garlic
gdpc
Ghemical
gOpenMol
GRASP
ICM Browser
Java Mage
JME Molecular Editor
JMol
SDSC MICE
MidasPlus
ModView
Molekel
MOLMOL
MolScript
Moviemol
O
PAOLA
PDB to VRML Converter
PREPI
PyMOL
Qmol
Rasmol (1, 2, 3, 4)
Raster3D
RasTop
ScienceGL
SCHAKAL
Spock
Turbo Frodo
VEGA ZZ
Viewmol
Viewer
Visualize
VMD
WinMGM2
XChemEdit/ChemEdit
XMakemol
XmMol
YMol
Network Visualization
ePath3D
Ospreys
ToPNet
TreeWiz
Tulip
        
Pharmacophore Modeling
FieldTemplater
LigandScout

Pharmacophore-Based Screening
FieldScreen

Pipelining/Workflow
InforSense
Pathways/White Carbon
Pipeline Pilot
Taverna
 
Programming
ASP
The Fortran Company
Fortran Library
Java
JavaScript
MMTK
Perl
PHP
Python
      
Properties /Parameters
Absolv
ADRIANA.code
Almond
Aqua Solutions
BIOCUBE
BioLoom (ClogP...)
Cranium
CODESSA
EPI Suite
CLIP
DISCON
Dragon
HYBOT-PLUS
Interactive Analysis
JOELib
mitools
      
Protein Interactions
DOT
Escher NG
HADDOCK
ProViz
   
Protein Properties
FIRST / MSU ProFlex

PEAT
pKaTool
 
Stereoisomer Generation
STERGEN
  
Superposition
FieldAlign
FlexS
GAMMA
LSim
MIPSIM
ROCS
   
Synthesis Design
ChIP
WODCA
     
Systems Biology
Cell Illustrator
Cytoscape
E-CELL
In Silico Cell
Ingenuity Pathways Analysis
SimWiz
Systems Biology Workbench
Teranode Design Suite
ToPNet
   
Tautomer Generation
TAUTOMER
   
Teaching
Molecular Conceptor
Modern Biopharmaceutics
Odyssey
  
Toxicity Prediction
Derek
MultiCASE
PASS (bioactivities)
TerraBase
  

Last Updated: July 9, 2008

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