Links for structure and ligand searches
Programs for working with ligands
Protein structures
RCSB Protein Data Bank
http://www.rcsb.org/pdb/index.html
Database for protein and DNA structures.
PDBsum
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum
Browser for the Protein Data Bank.
Electron Density Server at
Uppsala University
http://eds.bmc.uu.se/eds/
Loading electron densities of structures of PDB.
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Small
molecules
HIC-Up
http://alpha2.bmc.uu.se/hicup/
Database of small molecules of the Hetero-compound Information
Centre in Uppsala.
Cambridge Structural Database
(CSD)
http://www.ccdc.cam.ac.uk/products/csd/
Small molecule crystal structures.
Dundee PRODRG2 Server
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
Generating parameter files (GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O,
SHELX, HEX and MOL2) for small molecules.
Ligand Depot - Substructure
Search
http://ligand-depot-i.rutgers.edu/html/sketch.html
http://ligand-depot-i.rutgers.edu/html/index.html
Sketch a fragment of a ligand and search for it.
Macromolecular Structure Database
(MSD) - Ligand Chemistry
http://www.ebi.ac.uk/msd-srv/chempdb/cgi-bin/cgi.pl
Protein Ligand Database
http://www-mitchell.ch.cam.ac.uk/pld/
Ligand.Info
http://ligand.info/
Java-based tool: http://ligand.info/applet.html
Ligand.Info is a compilation of various publicly available databases of
small molecules such as
ChemBank,
ChemPDB,
KEGG,
NCI,
AKos GmbH, and
Asinex Ltd.
The total size of the Meta-Database is 1 million entries.
ChemBank
http://chembank.med.harvard.edu/
Compound Search: http://chembank.med.harvard.edu/compounds/
ChemBank is a freely available collection of data about small molecules
and resources for studying their properties, especially their effects
on biology.
KiBank
http://kibank.iis.u-tokyo.ac.jp/index.jsp
KiBank for in silico drug design. This database contains binding
affinity, structures of chemicals and target proteins, and many useful
links and information.
Binding Databse
http://www.bindingdb.org/bind/index.jsp
The BindingDB is a public, web-accessible database of measured binding
affinities for biomolecules, genetically or chemically modified
biomolecules, and synthetic compounds.
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Search
tools for
protein data
BRENDA
http://www.brenda.uni-koeln.de/
personal login: http://www.brenda.uni-koeln.de/logreg/login
Comprehensive Enzyme Information System.
Tadpole
http://uranos/sci_sw/Tadpole_1.2.9/index.html
Tool for automated protein data retrieval.
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Sequence
Alignment
Indonesia
http://xray.bmc.uu.se/dennis/
Program from the
Biomedical Centre in Uppsala for structure-based sequence alignments.
Java-based program which can read pdf-file for superimposing the
structures and creating a sequence alignment in various file-formats.
For starting the program: prepare indonesia / indonesia
Interactive Editor for Multiple
Sequence Alignments STRAP
http://www.charite.de/bioinf/strap/
Start:
/sw/mcm/app/java/jre1.5.0/javaws/javaws
http://www.charite.de/bioinf/strap/strap2.jnlp
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Programs
CORINA
http://www.mol-net.de/software/corina/index.html
Generation of 3D coordinates.
GOLD
http://gold.ccdc.cam.ac.uk/index.php
GOLD Interactive Web Trial
http://www.ccdc.cam.ac.uk/products/life_sciences/gold/
GOLD is a program for calculating the docking modes of small molecules
into protein binding sites.
insightII
Insight II can add hydrogens to ligands at different pH-values.
Marvin
http://www.chemaxon.com/marvin/
MarvinSketch and MarvinView for eg. SDF-files
MolProbity
http://kinemage.biochem.duke.edu/molprobity/index-king.html
MolProbity is a graphical user interface to many of the
macromolecule structure
analysis and validation programs produced in the
Richardson Lab at Duke
University.
OpenEye Scientific Software
http://www.eyesopen.com/
Quac Pac
http://www.eyesopen.com/products/applications/quacpac.html
May be usefull for calculating protonation state? Licence required!
Reduce
http://kinemage.biochem.duke.edu/software/reduce.php
Reduce is a program for adding hydrogens to a Protein DataBank (PDB)
molecular structure file.
Vida
http://www.eyesopen.com/products/applications/vida.html
/home/gabdourf/progs/VIDANC6
source env.com
Doesn't add hydrogens to a pdb file in the right way without any
further information (atomtypes, bonds, hybrydisation,...)
WatCH
http://www.bch.msu.edu/labs/kuhn/web/software/WatCH/doc.html
A tool for identifying conserved water sites and analyzing their degree
of conservation using heirarchical cluster analysis of superimposed
related Protein Data Bank structures.
WHATIF
http://swift.cmbi.kun.nl/whatif/
http://swift.cmbi.kun.nl/whatif/toc.html
Pro-Flex
XDrawChem 1.5
PDB2PQR
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Documentation
GOLD
GOLD 2.2
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Links
Links
to various programs
http://www.clarku.edu/faculty/mlei/chem_link.htm
U.S. Environmental protection Agency
http://www.epa.gov/nheerl/dsstox/Glossary.html
SMILES http://www.epa.gov/nheerl/dsstox/MoreonSMILES.html
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