PDBe-KB Collaborating Partner Resources

Protein and domain annotation resources

SCOP

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.

Pfam

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).

InterPro

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.

UniProt

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.

ProKinO

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.

Evolutionarily conserved sites

CATH-FunSites

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

ChannelsDB

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.

canSAR

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.

3DLigandSite

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.

M-CSA

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.

P2rank

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.

MetalPDB

Claudia Andreini

Functional annotation of metal-binding sites in 3D structures

Description: Functional annotation of metal-binding sites in 3D structures

Mutations and variations

Missense3D

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.

FoldX

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.

Protein binding sites

14-3-3-pred

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.

AKID

Manuela Helmer-Citterich

Predictions of phosphorylation sites for kinases in target proteins.

Description: Predictions of phosphorylation sites for kinases in target proteins.

CamKinet

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.

Biophysical parameters

DynaMine

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.

POPS

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.

Arpeggio

Tom Blundell

Calculations of interatomic interactions in protein structures

Description: Calculations of interatomic interactions in protein structures

COSPI-Depth

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

EFoldMine

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

MobiDB

Silvio Tossato

MobiDB provides consensus intrinsic disorder predictions.

Description: MobiDB provides consensus intrinsic disorder predictions.