| 3-D Protein Structure
Databases and Tools for 3-D Protein Structure Comparison and Alignment (USA) [e] - [e] AARS
Aminoacyl-tRNA Synthetase Database. A hypertext version of the database published in the 2000 Database Issue of the Nucleic Acids Research - [e] ABCdb
Archaeal and Bacterial ABC transporter database - [e] ASPD
ASPD (Artificial Selected Proteins/Peptides Database) is a curated database on selected from randomized pools proteins and peptides. Database access is realised by means of simple search system and SRS (Sequence Retrieval System). ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, ...) - [e] BindingDB
The Binding Database is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules - [e] BioMagResBank
BMRB's mission is to collect, archive, and disseminate (worldwide in the public domain) the important quantitative data derived from NMR spectroscopic investigations of biological macromolecules - [e] BLAST
Basic Local Alignment Search Tool finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families - [e] BMCD
Biological Macromolecule Crystallization Database and the NASA Archive for Protein Crystal Growth Data - [e] BMRB
BioMagResBank. A Repository for Date from NMR Spectroscopy on Proteins, Peptides and Nucleic Acids - [e] Brenda
The Comprehensive Enzyme Information System - [e] Cambridge Crystallographic Data Centre
CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high-quality information services and software - [e] CATH
A hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H) - [e] CDD
A Conserved Domain Database and Search Service - [e] ClustalW
... is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms - [e] Dali server
... is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is emailed back to you - [e] DExH/D protein database
... is an attempt to gather information about the DExH/D protein family with particular emphasis on the biochemical and functional characteristics of these proteins - [e] DIP
The DIP (TM) database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions - [e] DSSP database
... is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries - [e] EMBL Nucleotide Sequence Database
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications - [e] EMBL-Align Multiple Sequence Alignment Database
Sequence alignment data - [e] ENZYME
... is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided - [e] ExPASy Molecular Biology Server
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE - [e] EXProt
... a database for proteins with an experimentally verified function - [e] Fasta
Provides sequence similarity searching against nucleotide and protein databases using the FASTA programs. FASTA can be very specific when identifying long regions of low similarity especially for highly diverged sequences. You can also conduct sequence similarity searching against complete proteome or genome databases using the FASTA programs - [e] GPCRDB
Molecular Class-Specific Information System (MCSIS) project - [e] HEART-2DPAGE
The Human Myocardial Two-Dimensional Electrophoresis Protein Database is the two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database for human heart proteins. It contains data on proteins identified on the 2-D PAGE maps of ventricle and atrium of human heart - [e] Hits
... is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them - [e] Huge
The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on - [e] IMGT
... is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species - [e] IMGT/HLA Sequence Database
... provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT) - [e] InBase
The Intein Database and Registry - [e] InterPro
... is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences - [e] Isostar
... stores knowledge about intermolecular interactions in the form of scatterplots - [e] Kegg
Kyoto Encyclopedia of Genes and Genomes - [e] LIGAND
KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database currently consisting of COMPOUND, DRUG, GLYCAN, REACTION, RPAIR, and ENZYME databases - [e] Ligand Gated Ion Channel Database
Ligand-Gated Ion Channels are transmembrane proteins that can exist under different conformations, at least one forming a pore through the membrane connecting the two neighbour compartments - [e] MDB
... contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics - [e] MEROPS database
... is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them - [e] MetaFam
... is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases - [e] Metalloprotein Site Database & Browser
MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics - [e] MINT
... focuses on experimentally verified protein interactions mined from the scientific literature by expert curators - [e] Mirage
Molecular Informatics Resource for the Analysis of Gene Expression) is a web site dedicated to methodologies, tools, and technologies relating to gene expression information - [e] ModBase
A database of three-dimensional protein models calculated by comparative modeling - [e] MPsrch
... is a biological sequence sequence comparison tool that implements the true Smith and Waterman algorithm. It runs a search on a HP/COMPAQ cluster, using single and parallelised versions of the software - [e] MultAlin
Multiple sequence alignment - [e] MutaProt
Comparison of PDB files which differ by point mutations - [e] NDB
A repository of three-dimensional structural information about nucleic acids - [e] PDB
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease - [e] PDBsum
… provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them - [e] Peptaibol Database
A Bioinformatics resource - [e] Pfam
... is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) - [e] Phospho.ELM
... is a database of experimentally verified phosphorylation sites in eukaryotic proteins - [e] PIR
Protein Information Resource - [e] PKR
The Protein Kinase Resource has been redesigned and expanded with new content and cross-links with other online resources. In addition, we have introduced several new technologies to integrate information search, retrieval and visualization - [e] PlantsP
Functional Genomics of Plant Phosphorylation - [e] PPSEARCH
Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. EBI - [e] PredictProtein
... is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function - [e] PRINTS
... is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite - [e] ProDom
... is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases - [e] Promise
The Prosthetic groups and Metal Ions in Protein Active Sites Database - [e] Prosite
... consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them - [e] Protein Data Bank
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease - [e] Protein Explorer
Explore any 3D macromolecular structure model (PDB file) - [e] Protein Kinase Resource
PKR explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior - [e] Protein Mutant Database
PMD covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families - [e] RCSB Protein Data Bank
A Resource for Studying Biological Macromolecules - [e] RNase P Database
A compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information - [e] S/MARt DB
... collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human - [e] SBASE
Protein domain library - [e] SCOP
Structural Classification of Proteins - [e] SENTRA
A Database of Sensory Signal Transduction Proteins - [e] SeqAnalRef
... is a bibliographic reference data bank relative to papers dealing with sequence analysis. This data bank stores the references of articles from the expanding field of mathematical and computer analysis of biomolecular sequences - [e] Structure Finder
... is comprised of the search interfaces and the databases developed by the NDB Project - [e] SWISS-2DPAGE
Two-dimensional polyacrylamide gel electrophoresis database - [e] SWISS-MODEL Repository
... is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL - [e] SWISS-PROT
A curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases - [e] SYSTERS
Protein Family Database, Release 4: Large-scale Protein Clustering based on Sequence Similarity - [e] Telomerase Database
... is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein - [e] TRANSFAC
The Transcription Factor Database is a database containing mouse transcription factor genes and their related genes. It is intended to select transcription factor genes nonredundantly from entire Mouse genome - [e] Vida
... contains a complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures - [e] Webcutter
On-line tool for restriction mapping nucleotide sequences - [e] WPDB
The Protein Data Bank Through Microsoft Windows. Software zur PDB-Datenbank (USA) [e] - [e] | 
