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PROCOGNATE

http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html

Description :
Protein cognate ligands for the domains in enzyme structures

Binding MOAD

http://www.bindingmoad.org/

Description :
Binding Mother of All Databases: a database of protein-ligand crystal structures

LigAsite

http://www.scmbb.ulb.ac.be/Users/benoit/LigASite

Description :
Biologically relevant binding sites in proteins with known apo-structures

ProNIT

http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html

Description :
Thermodynamic data on protein-nucleic acid interactions

TarFisDock

http://www.dddc.ac.cn/tarfisdock/

Description :
Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.

eF-seek

http://ef-site.hgc.jp/eF-seek/index.jsp

Description :
eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

ET Report Maker

http://mammoth.bcm.tmc.edu/report_maker/

Description :
Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.

KFC Server

http://www.mitchell-lab.org/kfc

Description :
The KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.

MolSurfer

http://projects.villa-bosch.de/dbase/molsurfer/

Description :
Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

MultiBind

http://bioinfo3d.cs.tau.ac.il/MultiBind

Description :
Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.

PFP

http://pfp.technion.ac.il/

Description :
PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

PI2PE

http://pipe.scs.fsu.edu/

Description :
PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

FireDock

http://bioinfo3d.cs.tau.ac.il/FireDock/

Description :
The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.

AffinDB

http://www.agklebe.de/affinity

Description :
The Affinity Database AffinDB contains affinity data for protein-ligand complexes of the PDB. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure. As of Monday, November 28th, 2005, AffinDB contains 746 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex.

DDIB

http://www.ddib.org/

Description :
Protein domains, modules of amino acid sequence with specific evolutionarily conserved motifs, are the structural or functional units that participate in intermolecular interactions. Information about domain interactions has been accumulated, but are buried in literatures or scattered in various laboratories, thus, hard for users to find them.

The Database of Domain Interactions and Bindings (DDIB) collects information about domain-domain interactions and domain interactions with biological molecules such as nucleotides, peptides, inorganic ions, phospholipids. Some data were extracted By Natural Language Processing (NLP) method from publication abstracts included in MEDLINE, and some were collected from other public databases, research laboratories and individual scientists. In addition, DDIB includes many putative domain-domain interactions inferred from documented protein-protein interactions. To provide comprehensive knowledge of a domain, DDIB also includes relevant information from PFAM database, GO and KEGG. DDIB is freely accessible from http://www.ddib.org.

Aknowledgement :
This project was funded in part by the State Key Program of Basic Research of China (No. 001CB510209) and the 863 Hi-Tech Program (No. 2003AA231011).

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