PDBe-KB Collaborating Partner Resources
Protein and domain annotation resources
Alexey Murzin
The SCOP database, created by manual inspection and abetted by a battery of automated methods, [more...]
Description: The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
Alex Bateman
The Pfam database is a large collection of protein families, each represented by multiple sequence [more...]
Description: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
Rob Finn
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and [more...]
Description: InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
Maria J. Martin
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and [more...]
Description: The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
Natarajan Kannan
The Protein Kinase Ontology (ProKinO), is a protein kinase-specific ontology, which provides a controlled vocabulary [more...]
Description: The Protein Kinase Ontology (ProKinO), is a protein kinase-specific ontology, which provides a controlled vocabulary of terms, their hierarchy, and relationships unifying sequence, structure, function, mutation and pathway information on kinases.
Jose Maria Carazo
EMVS provides different quality and validation scores about cryo-Electron Microscopy maps and their corresponding atomic [more...]
Description: EMVS provides different quality and validation scores about cryo-Electron Microscopy maps and their corresponding atomic models.
Joanna Sulkowska
The database provides information regarding the presence of knots or slipknots on protein chains and, [more...]
Description: The database provides information regarding the presence of knots or slipknots on protein chains and, in the case of their presence, also the type of the knot/slipknot and its position in the chain.
Roland Dunbrack
KinCore provides conformational annotations for protein kinase structures.
Description: KinCore provides conformational annotations for protein kinase structures.
Evolutionarily conserved sites
Christine Orengo
CATH-FunSites are groups of amino acid residues that are evolutionarily conserved within a CATH FunFam, [more...]
Description: CATH-FunSites are groups of amino acid residues that are evolutionarily conserved within a CATH FunFam, i.e. proteins sharing the same function and hence, are most likely to be functionally important.
Small-molecule sites
Jaroslav Koča
ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in [more...]
Description: ChannelsDB is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank. As such, it is a unique service for channel-related analyses.
Bissan Al-Lazikani
canSAR is an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural [more...]
Description: canSAR is an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions.
Mark Wass
3DLigandSite is an automated method for the prediction of ligand binding sites.
Description: 3DLigandSite is an automated method for the prediction of ligand binding sites.
Janet Thornton
M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic [more...]
Description: M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes.
David Hoksza
P2Rank is a machine learning based method for prediction of ligand binding sites from protein [more...]
Description: P2Rank is a machine learning based method for prediction of ligand binding sites from protein structure.
Claudia Andreini
Functional annotation of metal-binding sites in 3D structures
Description: Functional annotation of metal-binding sites in 3D structures
Nir London
Covalentizer provides candidates for covalent analogues of small molecules.
Description: Covalentizer provides candidates for covalent analogues of small molecules.
Mutations and variations
Michael Sternberg
Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to [more...]
Description: Missense3D predicts the structural changes introduced by an amino acid substitution and is applicable to analyse both PDB coordinates and homology-predicted structures.
Luis Serrano
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to [more...]
Description: FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
Juan Fernández-Recio, Iain H Moal
SKEMPI provides binding free energy changes upon mutation for structurally resolved protein-protein interactions, including changes [more...]
Description: SKEMPI provides binding free energy changes upon mutation for structurally resolved protein-protein interactions, including changes in kinetics, as well as enthalpy and entropy changes for a subset of mutations.
Jiri Damborsky
FireProt DB provides the stability effects of single-point mutants.
Description: FireProt DB provides the stability effects of single-point mutants.
Protein binding sites
Geoff Barton
14-3-3-Pred is a webserver that predicts 14-3-3-binding sites in proteins by combining predictions from three [more...]
Description: 14-3-3-Pred is a webserver that predicts 14-3-3-binding sites in proteins by combining predictions from three different classifiers: ANN, PSSM SVM, as wll as a consensus predictor. 14-3-3-Pred provides prediction scores as well as information on the phosphorylation state of the respective Ser/Thr.
Manuela Helmer-Citterich
Predictions of phosphorylation sites for kinases in target proteins.
Description: Predictions of phosphorylation sites for kinases in target proteins.
Toby Gibson
CaMKinet is a Calcium/Calmodulin-dependent protein kinases (CaMKs) and their substrates database. CaMKs and their allies [more...]
Description: CaMKinet is a Calcium/Calmodulin-dependent protein kinases (CaMKs) and their substrates database. CaMKs and their allies constitute a large family of Serine/Threonine kinases.
Lennart Martens, Wim Vranken
Scop3P provides Human phosphorylation sites identified by re-processing large scale public proteomics datasets.
Description: Scop3P provides Human phosphorylation sites identified by re-processing large scale public proteomics datasets.
Emmanuel D Levy
3DComplex provides protein-protein interaction interfaces.
Description: 3DComplex provides protein-protein interaction interfaces.
Biophysical parameters
Wim Vranken
DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input.
Description: DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input.
Franca Fraternali
POPSCOMP is a method to analyse interactions between individual complex components of proteins and/or nucleic [more...]
Description: POPSCOMP is a method to analyse interactions between individual complex components of proteins and/or nucleic acids by calculating the solvent accessible surface area (SASA) buried upon complex formation.
Tom Blundell
Calculations of interatomic interactions in protein structures
Description: Calculations of interatomic interactions in protein structures
M.S. Madhusudhan
Server for computing/predicting depth, cavity sizes, ligand binding sites and pKa
Description: Server for computing/predicting depth, cavity sizes, ligand binding sites and pKa
Wim Vranken
Sequence-based predictions of the residues that start to fold independently in proteins
Description: Sequence-based predictions of the residues that start to fold independently in proteins
Silvio Tossato
MobiDB provides consensus intrinsic disorder predictions.
Description: MobiDB provides consensus intrinsic disorder predictions.
Nathalie Reuter
WEBnm@ provides flexibility prediction in the form of the normalized displacement of each amino acid [more...]
Description: WEBnm@ provides flexibility prediction in the form of the normalized displacement of each amino acid in the structure. The displacement is predicted by performing Normal mode analysis (NMA) using an elastic network model (ENM) on each single PDB file. Note that only the first 200 lowest-frequency normal modes are used to calculate the displacement.