Druggable Genome (minus olfactory and taste receptors / plus ligandome) (thanks to Hong Xu and John Tomfohr)
Human Plasma Membrane Receptome (HPMR)
Kinbase - Kinase database
Ligandome - (genomically encoded receptor activating proteins) (thanks to John Tomfohr)
Ligand Gated Ion Channel Database
MACiE - a database of enzyme reaction mechanisms
Sigma-RBI Receptor and Enzyme Handbook
SUPERFAMILY - provides protein domain assignments, at the SCOP 'superfamily' level, for the predicted protein sequences in over 400 completed genomes
SuperTarget - integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins
Therapeutic Target Database - A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets
Tumor Gene Family Databases - contains information about genes which are targets for cancer-causing mutations; proto-oncogenes and tumor supressor genes
xPharm (subscription) - comprehensive drug target database supplement with results taken from the literature
3D Complex - the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph
3D-Jigsaw - This server builds three-dimensional models for proteins based on homologues of known structure
3D-Structure Data Mining - Collection of small molecule structure databases
AffinDB - Affinity database for protein-ligand complexes
AutoDock - a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
BallView - standalone molecular modeling and visualization application
BDT - Autogrid/Autodock software download
BindingDB - a public, web-accessible database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds
Catalytic Site Atlas - a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure
Cambridge Crystallography Data Center - The world repository of small molecule crystal structures
CAVER - provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures
Distill - Prediction of protein structure features
DrugScore - a web-based user interface for the knowledge-based scoring functions DrugScoreCSD and DrugScorePDB. DrugScoreONLINE enables you to score protein-ligand complexes of your interest and to visualize the per-atom score contributions
EBI-MSD - The "Ligand Chemistry" service provides web access to the "ligands and small molecule dictionary" of the MSD database developed by the MSD group at EBI
ESyPred3D - a new automated homology modeling program
EzCatDB - includes catalytic mechanisms of enzymes in terms of sequences and tertiary structures of enzymes, and proposed catalytic mechanisms, along with ligand structures
FCP - Functional Coverage of the proteome. Database of proteins that have structures deposited in PDB
FeatureMap3D - Each query sequence is aligned to the best hit in PDB. The hit is visualized by mapping the alignment onto the PDB structure using color-coding for match/mismatch gaps etc. User provided feature annotation (e.g. phophorylation sites, evolutionary interesting sites or pattern of alternative splicing) can also be mapped onto the PDB structure.
FireDB - a databank that contains the most comprehensive and detailed repository of known functionally important residues, bringing together both ligand binding and catalytic residues in one site
Garrett Morris Molecular Docking Site - Huge collection of molecular docking resources
GENO3D - homology modeling server
GFscore - A General Non-Linear Consensus Scoring Function for High-Throughput Docking
HIC-Up - Hetero-compound Information Centre
ICM Browser - provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.
iFold - a web portal for interactive protein folding/unfolding simulations.
iMolTalk - an interactive, Internet-based service for computational analyses in Structural Biology
Jackal - a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package nest
KiBank - database contains binding affinity, structures of chemicals and target proteins, and many useful links and information.
kinDOCK - erver allows comparative docking of ligands into the ATP-binding site of a protein kinase (target)
Laboratoire de Bioinformatique du Medicament - a collection of virtual screening tools for identifying potential ligands
LigProf - A simple tool for in silico prediction of ligand-binding sites
MAGOS - an automated modelling of your query protein coupled to the creation of a hierarchical and annotated Multiple Alignment of Complete Sequences
MEDock - a Maximum-Entropy based docking web server for efficient prediction of ligand binding sites
MOAD - a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. hence, we call it the Mother of All Databases (MOAD)
ModBase - a database of three-dimensional protein models calculated by comparative modeling
MODWEB - Server for Comparative Protein Structure Modeling. Web-based application using Modeller software
MolMovieDB - Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis
MolProbability - structure validation and all-atom contact analysis for nucleic acids and their complexes
Nestor3D - a free software allowing the multiple alignment of a set of protein structures containing either ligands, prosthetic groups or PROSITE patterns
P-cats - ocate the catalytic residues in a protein from its sequence and structure
PDBbind - a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB)
PDBsite - provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions) in the Protein Data Bank
PBD Metrics - a summary of the protein structures deposited in the Protein Data Bank (PDB). It offers a vast collection of descriptors and means to recover specific PDB files. PDB-Metrics is a powerful tool for the bioinformatics researcher to analyze the PDB's collection of protein structure descriptions from a variety of perspectives, and recover specific files using a repertoire of alternate criteria.
PIBase - A Comprehensive Database of Structurally Defined Interfaces in Proteins
PocketDepth - binding site prediction which is geometry based and uses a depth based clustering
Pocket-Finder - search your protein in silico for ligand binding sites
PredictProtein - a service for sequence analysis, and structure prediction
PRODRG2 - convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2
PROFbval - a method for predicting residue mobility based on amino-acid sequence
ProSAT2 - a server to select and group residue based annotations and explore them interactively on a 3D structure of a protein
Protein Data Bank - protein structure repository
Protinfo -collection of protein analysis tools
Q-SiteFinder - Ligand binding site prediction
RELIC - (REceptor LIgand Contacts) - a publicly accessible bio-technology system that utlilizes web technology, traditional programming and a relational database to process and manipulate the experimental data of affinity selected peptides
Ressource Parisienne en Bioinformatique Structurale - Collection of structural biology tools and resources
sc-PDB - an annotated database of druggable binding sites from the Protein Data Bank
SCOPEC - maps catalytic function to domain structure using the structural domain information in the SCOP domain database, full length sequence information from Swiss-Prot, and verified functional information from the Enzyme Classification (EC) scheme
SCOWLP - Structural Characterization Of Water, Ligands and Proteins
Simulaid - simulation setup utilities for structural biology
SitesBase - a database of known ligand binding sites within the PDB which is navigable by PDB identifier or ligand 3 letter code
SRS 3D - allows users to easily and rapidly find all related structures for a given target sequence; structures can then be viewed together with sequences, alignments and sequence features (currently from UniProt, InterPro and PDB)
Swiss-Model - homology modeling server
TarFisDock - a web server for identifying drug targets with docking approach
TASSER-Lite - a comparative protein structure modeling tool
UCSF Dock - Molecular Docking software
UofI Theoretical and Computational Biophysics Group - Protein structure dynamics tools
VISSA - (VIsualize Structure Sequence Alignment) is a program that can visualize both multiple seeuqnce alignment and 3D structure and can also map residues from alignment onto 3D structure and vice versa
WhatIF - collection of tools to prepare proteins and molecules for in silico docking studies
ZINC - a free database of commercially-available compounds for virtual screening. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats