3D-Ali -- Database of aligned protein structures and related sequences
3Dee -- Protein domain definition
AGADIR -- Predicts the helical content of peptides
ALIGN
-- Compendium of protein sequence alignments
ASTRAL -- Databases and tools for analyzing protein structures and sequences. Partially derived from the Structural Classification of Proteins (SCOP) database
Backbone-Dependent Rotamer Libraries -- Rotameric states of protein side chains. Used for analyses by Protein Sidechain Webpage
Biomolecular Interaction Network Database (BIND) -- Database at the Samuel Lunenfeld Research Institute that aims to encompass "the growing network of protein and other biomolecular interactions."
BioImage -- Searchable database of multidimensional biological images (macromolecules and cellular structures)
Biotech Validation Suite -- Protein structure verification
BLAST (GenomeNet)
BLAST (NCBI)
BLOCKS -- database of conserved regions in protein sequences
BMM Domain Assignment -- Tool for assigning domains based on sequence and published data
CAMbridge database of Protein Alignments organised as Structural Superfamilies (CAMPASS) -- Collection of sequence alignments of protein (domain)s that belong to superfamilies, as defined by SCOP
CATH -- Protein structure classification based on hierarchy of class(C), architecture(A), topology(T) and homologous superfamily (H)
COGs -- NCBI Clusters of Orthologous Groups (of proteins)
COILS -- Prediction of coiled coil regions in proteins
Combinatorial Extension -- 3-D Protein structure comparison and alignment of two sequences using Protein Data Bank (PDB)
DALI -- compares protein structures in 3D using coordinates of a query protein structure against those in the Protein Data Bank (PDB)
DAS -- Transmembrane helix prediction
DNA-Binding Protein Full Search -- Search of the nucleic acid database to find protein-DNA strcutures
DSSP -- Database of secondary structure assignments for all proteins in the Protein Data Bank (PDB)
Enzyme Structures Database -- Database of enzyme structures from the PDB
Family Pairwise Search (FPS) -- a mechanism for comparing a protein sequence against a family of sequences or structures in the SCOP, Pfam or PROSITE databases
Finding 3D Similarity -- identifies 3D structures using combinatorial extension and compound likeness
FSSP -- Protein fold classification database based on structure-structure alignment of proteins. Contains structural all-against-all alignments for PDB
HSSP -- database of protein secondary structures derived by aligning to each protein of known structure all sequences deemed homologous
IDEAS
Library of Protein Family Cores -- Structural alignments of protein families and computed average core structures for each family. Categorized according to spatial variation values
Macromolecular Structure Database -- database of quaternary structures
ModBase -- database of comparative proteins structure models
Modules -- Information and research tools on mobile protein domains
Molecular Modelling Database (MMDB) -- searchable structural database of over 10,000 domains of macromoles
Molecules R Us -- Tool for accessing molecular structure data contained within the Brookhaven Protein Data Bank (PDB)
MOTIF
NRL 3D Structure Database -- produced by PIR from sequence and annotation information in the Protein Databank (PDB)
OLDERADO -- database of the core atoms, domains and representative structures from all current NMR-derived protein structures in the PDB
OWL -- Non-redundant composite protein database of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation), and NRL-3D.
PairCoil -- predicts the location of coiled-coil regions within protein or peptide sequence
PDB at a Glance -- classification of the current release of the Brookhaven Protein Databank (PDB) with links to relevant data
PDBSUM -- Summaries and structural analyses of PDB files
Pfam -- database of multiple protein sequence alignments and hidden Markov models covering many common protein domains
Pratt Pattern Discovery -- searches for patterns conserved in a set of protein sequences. User can specify type of pattern searched for, and number of matches to be reported
PredictProtein -- Protein sequence analysis and structure prediction
PRINTS -- database of conserved motifs used to characterise a protein family
PRODOM -- database of protein domains
PROSITE -- Database of protein families and domains
Protein Data Bank (PDB) -- databank of 3D protein structures primarily determined experimentally by X-ray crystallography and NMR
PROSPECT
Protein Loop Classification
Protein-Protein Interface Database -- Database of all protein-protein interfaces present in the PDB
ProtFam -- Classification by protein (super)family and homology domains. Multiple alignments for superfamilies, families, and domains.
Protein Sidechain Webpage -- Includes backbone-independent and backbone-dependent rotamer libraries and a program for making sidechain conformation predictions for proteins
Protein Structure Initiative -- Structural Genomics Project that aims to determine the 3D structure of all proteins
Protein Structure Prediction Center
ProtoCall - Search engine for protein identification from MS data (requires Internet Explorer 5.5 or higher).
ReLiBase -- Receptor-ligand complex database
RESID -- protein post-translational modifications with descriptive, chemical, structural and bibliographic information
ScanProsite
SCRate -- Tool to evaluate the accuracy of alignment of protein sequences with very low sequence identity
Sequence and Structure Searching Site
SLoop Database
SSCP -- Predicts secondary structural content from amino acid composition
Structural Classification of Proteins (SCOP) -- aims to describe structural and evolutionary relationships between proteins whose structure is known. Provides a broad survey of all known protein folds
Swiss-Model -- Automated comparative protein structure modelling
Swiss-Prot 3DCrunch Database -- Tool for searching through 3D protein structures automatically generated from the Swiss-Prot database
Teiresias -- Identifies patterns in protein sequences
TMHMM -- Transmembrane helix prediction
TOP Structural Similarity Searches -- Search for structural similarity using SCOP database.
TOP 3D Similarity Searches -- Search for 3D structure similarity using PDB information
TOPS -- Protein topology database
UCLA-DOE Structure Prediction Server
WD-repeat Family of Proteins -- proteins that contain four or more copies of the tryptophan-aspartate repeat
X-Ray Anomalous Scattering Database -- Introductory tutorial to anomalous scattering in X-ray crystallography.
