Computational Science Software #2

■ --- Docking software ----------------------------

ParaDockS
http://europa.pharmazie.uni-halle.de/joomla/

DockingServer
http://www.dockingserver.com/

PLANTS / University of Konstanz
http://www.tcd.uni-konstanz.de/research/plants.php

AutoDock / Scripps Research Institute
http://autodock.scripps.edu/

DOCK / University of California San Francisco
http://dock.compbio.ucsf.edu/

Molegro Virtual Docker / Molegro ApS(University of Aarhus)
http://www.molegro.com/

GRAMM / University of Kansas
http://vakser.bioinformatics.ku.edu/main/resources_gramm.php

Hex Protein Docking / Dave Ritchie (LORIA)
http://www.loria.fr/~ritchied/hex/

HADDOCK / Utrecht University
http://www.nmr.chem.uu.nl/haddock/

3D-DOCK,ZDOCK,ESCHER,ROSETTA,DOT.

eHiTS / SimBioSys Inc
http://www.simbiosys.ca/ehits

ICM Pro / Molsoft LLC
http://www.molsoft.com/icm_pro.html

Glide / Schrödinger, LLC
http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6&cID=0

MOE / Chemical Computing Group Inc.
http://www.chemcomp.com/

GOLD / The Cambridge Crystallographic Data Centre
http://www.ccdc.cam.ac.uk/products/life_sciences/gold/

FlexX / BioSolveIT GmbH
http://www.biosolveit.de/flexx/

■ --- QSAR --------------------------------

McQSAR
http://users.abo.fi/mivainio/mcqsar/

CDKDescUI
http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkdesc.html

CDK Descriptor Calculator GUI
http://rguha.net/code/java/cdkdesc.html

eHITS LASSO
http://www.simbiosys.ca/ehits_lasso/index.html

SAMFA
http://pubs.acs.org/doi/suppl/10.1021/ci800009u

QSARPro
http://www.vlifesciences.com/products/QSARPro/qsar_pro.htm

Parameter Client
http://www.vcclab.org/
http://www.vcclab.org/lab/pclient/
http://146.107.217.178/lab/pclient/

E-Dragon
http://www.vcclab.org/lab/edragon/
http://146.107.217.178/lab/edragon/

MODEL - Molecular Descriptor Lab
http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi

PreADMET
http://preadmet.bmdrc.org/preadmet/index.php
http://preadmet.bmdrc.org/preadmet/query/query1.php

Leadscope
http://www.leadscope.com/

http://www.support-vector-machines.org/SVM_soft.html

■ ---- homology modeling ----------------------------

http://en.wikipedia.org/wiki/Protein_structure_prediction_software

3D-PSSM
http://www.sbg.bio.ic.ac.uk/~3dpssm/

WebPDB
http://reccr.chem.rpi.edu/Software/WebPDB/WebPDB-index.html

Modeller is one possibility, its free of chartge for academic and non-profit
institutions
http://salilab.org/modeller/

Also the swiss-model might be interesting. You can use it via a web-interface
http://swissmodel.expasy.org//SWISS-MODEL.html

For side chain modelling I recommend SCWRL (also free for academic institutions):
http://dunbrack.fccc.edu/SCWRL3.php

■ --- DFT ------------------------------------

PARSEC
http://parsec.ices.utexas.edu/

Elk FP-LAPW
http://elk.sourceforge.net/

■ --- Modeling / Viewer ------------------------------------

Zodiac
http://www.zeden.org/

Avogadro
http://sourceforge.net/projects/avogadro/

Ascalaph Quantum
http://www.agilemolecule.com/Ascalaph/Ascalaph_Quantum.html

mol2ps
http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html