PDBe-KB Collaborating Partner Resources
Protein, domain and annotation resources
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
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.
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.
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 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 is an automated method for the prediction of ligand binding sites.
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.
Mutations and variations
Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations.
Protein binding sites
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.
NoD is a predictor of nucleolar localisation sequences (NoLSs) in proteins. NoLSs are short, basic motifs that localise proteins to the nucleolus, a sub-compartment of the nucleus.
Manuela Helmer Citterich
Predictions of phosphorylation sites for kinases in target proteins
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.
DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input.
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.