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A Protein Classification Benchmark collection for machine learning
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| Use standard datasets to compare protein classification by different machine learning methods.
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A fully automatic evolutionary classification of protein folds -- Dali Domain Dictionary version 3
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| Search information on numerical taxonomy of all known structures in the Protein Data Bank (PDB).
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A rapid classification protocol for the CATH Domain Database to support structural genomics
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| Search for information on protein structures, domains, folds, and structural classifications.
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ADDA -- a domain database with global coverage of the protein universe
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| Search for information on protein domain family.
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Applications for protein sequence–function evolution data -- mRNA/protein expression analysis and coding SNP scoring tools
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| Conduct protein classification, expression analysis and SNP function screening.
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BIOZON -- a hub of heterogeneous biological data
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| Search for a wide range of protein data and information through this unified biological database.
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Berkeley Phylogenomics Group
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| Resources for structural phylogenomic analysis.
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CD-Search -- Protein Domain Annotations on the Fly
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| Detect structural and functional domains in protein sequences.
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CDD -- A curated Entrez database of conserved domain alignments
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| Identify conserved domain in a protein sequence.
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CHOP -- Parsing proteins into structural domains
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| Chop proteins into domain-like fragments.
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CluSTr -- The database of SWISS-PROT+TrEMBL protein clusters
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| Study protein classification based on an automatic classification of SWISS-PROT+TrEMBL proteins into groups of related proteins.
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DAhunter -- Domain Architecture hunter
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| A retrieval tool for conserved protein domain architecture.
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DIAL -- a web-based server for the automatic identification of structural domains in proteins
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| Automatically identify protein structural domains given the three-dimensional coordinates of a protein.
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DOMAC -- a hybrid protein domain prediction server
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| An accurate protein domain prediction server.
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DOUTfinder — identification of distant domain outliers using subsignificant sequence similarity
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| Detect distantly related protein domains.
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FISH — family identification of sequence homologues using structure anchored hidden Markov models
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| Identify homologous protein domain sequences.
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FunShift -- a database of function shift analysis on protein subfamilies
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| Search for information on functional shift within protein family.
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GeneSpeed -- protein domain organization of the transcriptome
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| Study the PFAM protein domain content of the transcriptome (Unigene Database) for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans.
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GeneTrees -- a phylogenomics resource for prokaryotes
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| Search for pre-computed alignments and phylogenetic trees for all protein sequences from 325 fully sequenced and annotated prokaryote genomes.
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Hits -- Access to databases of predicted protein sequences
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| Search and investigate protein motif sequences.
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InterProScan -- protein domains identifier
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| Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.
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KOG - Eukaryotic Orthologous Groups of proteins
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| Search Clusters of Orthologous Groups of protein (COGs) for seven (nearly) complete eukaryotic genomes. |
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MINER -- software for phylogenetic motif identification
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| Identify phylogenetic motifs in protein sequences. |
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MulPSSM -- a database of multiple position-specific scoring matrices of protein domain families
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| Search for position-specific scoring matrices for a large number of sequence and structural families of protein domains.
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MultiPhyl -- A high-throughput phylogenomics webserver using distributed computing
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| Upload multiple amino acid or nucleotide alignments and perform the tasks of ML model selection, tree searching, and bootstrapping.
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MyHits -- An Interactive Resource for Analyzing Protein Sequences
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| An integrated service dedicated to the analysis of protein sequences.
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NEWT -- a new taxonomy portal
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| Search taxonomy data for the complete set of species represented in SWISS-PROT, as well as those stored at the NCBI.
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PANDIT -- an evolution-centric database of protein and associated nucleotide domains with inferred trees
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| Search for multiple sequence alignments and phylogenetic trees covering many common protein domains. |
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PANTHER -- A browsable database of gene products organized by biological function, using curated protein family and subfamily classification
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| Browse and search proteins based on their biological functions. |
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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
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| Calculate maximum likelihood phylogenies from DNA and protein sequences.
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PIRSF -- Protein family classification system at the Protein Information Resource
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| To analyze protein phylogenetic profiles, to reveal functional convergence and divergence, and to identify relationships between homeomorphic families, domains and structural classes.
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POWER -- PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis
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| Perform user-friendly pipeline phylogenetic analysis of protein or DNA sequences. |
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PRECISE -- a Database of Predicted and Consensus Interaction Sites in Enzymes
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| Search for information on interactions between the amino acid residues of an enzyme and its ligands.
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PRED-GPCR -- GPCR Recognition and Family Classification Server
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| Recognize and classify G-protein coupled receptors (GPCRs) at the family level. |
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PRINTS and its automatic supplement, prePRINTS -- A compendium of protein fingerprints
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| Search for protein fingerprints.
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PRODOC -- a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
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| Search and compare functional domain assignments for proteins encoded in 192 complete genomes.
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PairsDB -- atlas of protein sequence space
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| Explore protein sequences and their similarity relationships.
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Pfam -- Protein Families Database
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| A comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models.
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Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics
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| Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.
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PhyloDome —- visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets
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| Visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.
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Phylocom -- software for the analysis of phylogenetic community structure and trait evolution
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| Calculates numerous metrics of phylogenetic community structure and trait similarity within communities.
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Phylogeny.fr -- robust phylogenetic analysis for the non-specialist
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| A web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.
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PipeAlign -- a new toolkit for protein family analysis
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| Use this protein family analysis tool to search for sequence homologues in protein and 3D structure databases, the definition of the hierarchical relationships within and between subfamilies.
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ProDom and ProDom-CG -- Tools for protein domain analysis and whole genome comparisons
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| Search and analyze protein domain families.
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ProtoMap -- Automatic classification of protein sequences and hierarchy of protein families
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| Classify protein sequences.
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ProtoNet -- Hierarchical classification of the protein space
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| Classify proteins using automatic hierarchical clustering of the SWISS-PROT protein database.
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S4 -- structure-based sequence alignments of SCOP superfamilies
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| Search for structure-based sequence alignments of domains in SCOP protein superfamilies.
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SCOPEC -- Mapping of catalytic function to domain structure
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| Search for information on enzyme catalytic domains. |
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SEARCHPKS -- a program for detection and analysis of polyketide synthase domains
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| Detect and analyze polyketide synthase (PKS) domains in a polypeptide sequence.
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SH3-Hunter -- discovery of SH3 domain interaction sites in proteins
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| Identify putative SH3 domain interaction sites on protein sequences.
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SIMAP -- structuring the network of protein similarities
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| Search for pre-computed similarity matrix of protein sequences.
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SMART 5 -- domains in the context of genomes and networks
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| To identify and annotate protein domains.
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SUPFAM — A database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families
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| Analyze and compare homologous protein families in a multiple sequence alignment database of either known or unknown structure.
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SVM-Prot -- web-based support vector machine software for functional classification of a protein from its primary sequence
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| Classify a protein into functional family from its primary sequence.
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The COG database -- phylogenetic classification of proteins from complete genomes
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| Search information on phylogenetic classification of proteins encoded in complete genomes of different organisms. |
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The InterPro Database
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| Identify protein family, domains, patterns, motifs, protein families, and functional sites.
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The MPI Bioinformatics Toolkit for protein sequence analysis
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| Conduct protein sequence and structure analysis using a suite of software tools. |
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The PredictProtein server
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| Predict protein structure and function based on protein sequence. |
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The SBASE domain sequence library -- Domain architecture prediction
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| Search for protein domain sequences, structures, functions,etc.
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The SYSTERS Protein Family Database in 2005
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| Partition of the whole protein sequence space by a fully automatic procedure.
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The TIGRFAMs database of protein families
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| Search for curated information of protein families based on Hidden Markov Models.
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TreeDomViewer -- a tool for the visualization of phylogeny and protein domain structure
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| Visualize structure and phylogeny of protein domains.
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Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
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| Use several Web servers to conduct various protein modeling and protein structure analysis. |
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iProClass -- An integrated database of protein family, function and structure information
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| Search for integrated and comprehensive information on family relationships and structural/functional features of proteins.
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