European Bioinformatics Institute

Proteins

Popular services

		UniProt: The Universal Protein Resource The gold-standard, comprehensive resource for protein sequence and functional annotation data.
		PRIDE: The Proteomics Identifications Database An archive of protein expression data determined by mass spectrometry.
		InterPro A database for the classification of proteins into families, domains and conserved sites.
		Pfam A database of hidden Markov models and alignments to describe conserved protein families and domains.
		Clustal Omega A new multiple sequence alignment tool using HMM-HMM profiles, suitable for medium-large alignments.
		InterProScan InterProScan is a software package that allows users to search their sequences against the InterPro database's predictive protein signatures.
		Clustal Phylogeny Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.
		NCBI BLAST [protein] Fast local similarity search tool for protein sequence databases.
		Protein Data Bank in Europe The European resource for the collection, organisation and dissemination of 3D structural data (from PDB and EMDB) on biological macromolecules and their complexes.

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		CENSOR A tool that screens query sequences against a reference collection of repeats.
		Clustal Omega A new multiple sequence alignment tool using HMM-HMM profiles, suitable for medium-large alignments.
		Clustal Phylogeny Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.
		ClustalW2 Multiple sequence alignment with ClustalW2.
		DbClustal Create a multiple sequence alignment from a protein BLAST result.
		Distributed Annotation System (sensu protein sequences) DAS provides client-side integration of protein sequence annotation.
		EMBOSS Tools Selected EMBOSS tools for sequence analysis, providing: pairwise sequence alignment, sequence format conversion, sequence translation and back-translation, and sequence statistics.
		Enzyme Portal: Integrated enzyme data from EMBL-EBI resources Integrated functional, sequence, nomenclature, substrate, product and cofactor data for enzymes.
		FASTA [protein] Similarity search tool for protein sequence databases.
		FASTM [protein] Peptide fragment similarity search tool
		FingerPRINTScan Search PRINTS with a protein query sequence.
		GGSEARCH [protein] Optimal global similarity search tool to search protein databases for sequences homologous to your query.
		GLSEARCH [protein] Optimal global-query, local-database, similarity search tool to search protein databases for sequences homologous to your query.
		IntEnz: Integrated relational enzyme database Reference enzyme nomenclature and function.
		InterPro A database for the classification of proteins into families, domains and conserved sites.
		InterProScan InterProScan is a software package that allows users to search their sequences against the InterPro database's predictive protein signatures.
		Kalign Very fast multiple sequence alignment tool, suitable for large alignments.
		LALIGN [protein] LALIGN finds internal duplications by calculating non-intersecting local alignments of protein or nucleotide sequences.
		MAFFT Multiple sequence alignment tool that uses Fast Fourier Transforms, suitable for medium alignments.
		MEROPS A database of proteolytic enzymes, their substrates and inhibitors.
		MUSCLE Accurate multiple sequence alignment tool, especially good with proteins. Suitable for medium alignments.
		MView Transform a sequence similarity search result into a multiple sequence alignment or reformat a multiple sequence alignment.
		NCBI BLAST [protein] Fast local similarity search tool for protein sequence databases.
		Patent databases Non-redundant patent sequence databases providing access to full-text patent documents.
		Pfam A database of hidden Markov models and alignments to describe conserved protein families and domains.
		Phobius Tool to predict transmembrane topology and signal peptides from the amino acid sequence of a protein.
		Pratt - Pattern Matching Discover patterns in unaligned protein sequences.
		PRIDE: The Proteomics Identifications Database An archive of protein expression data determined by mass spectrometry.
		PROSITE Scan Search a protein query sequence for protein motifs using the patterns and profiles in PROSITE.
		Protein Data Bank in Europe The European resource for the collection, organisation and dissemination of 3D structural data (from PDB and EMDB) on biological macromolecules and their complexes.
		PSI-BLAST Fast iterative motif-based similarity search tool for proteins
		PSI-Search Highly accurate iterative motif-based similarity search tool for proteins.
		RADAR Rapid Automatic Detection and Alignment of Repeats in protein sequences
		Readseq Conversion between common biological sequence formats.
		Rhea: Enzyme-catalysed reactions A curated database of enzyme-catalysed reactions.
		SAPS - Statistical Analysis of Protein Sequences Evaluate a wide variety of protein sequence properties
		Sequence Checksum Generator Generation of checksums for protein and nucleotide sequences.
		SRS - Sequence Retrieval System Advanced querying of EMBL-EBI databases.
		SSEARCH [protein] Smith-Waterman sequence similarity search against protein databases.
		T-Coffee Consistency-based multiple sequence alignment tool that attempts to mitigate the pitfalls of progressive alignment methods. Suitable for small alignments.
		UniProt: The Universal Protein Resource The gold-standard, comprehensive resource for protein sequence and functional annotation data.
		UniSave A historical repository of UniProtKB entry versions.
		Web Services Programmatic access to various data resources and analysis tools via Web Services technologies.
		WU-BLAST [protein] Sequence similarity search of protein databases with WU-BLAST.

Project websites

		IMPACT
		Reference Proteomes

Proteins

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