Protein Structure Resources

Protein Structure Bioinformatics Resources
An arbitrary subset gathered by Eric Martz
provided as a supplement to Protein Explorer.
EMail suggestions to me.

Books on protein structure and crystallography.
CAPRI: Critical Assessment of PRedicted Interactions, to assess the capacity of protein-protein docking methods to predict protein-protein interactions.
CASP: Critical Assessment of techniques for protein Structure Prediction. An annual competition in which information is solicited from X-ray crystallographers and NMR spectroscopists on structures about to be solved. Before the empirical structures are known, modelers submit structure predictions in three categories: comparative modeling, fold recognition or threading, and ab initio folding. Includes Ten Most Wanted, to provide structural and functional insights into biologically important proteins, particularly those that are intractable to experimental structural determination.
Combinatorial Extension, Finding 3D similarities in protein structures without reference to sequence. Automated intelligent alignment of protein chains (ligands are discarded).
ConSurf, Automated identification of functional regions in proteins of known 3D structure based upon evolutionary conservation.
Dali: Compares structure of submitted coordinates with those in the Protein Data Bank, without reference to sequence. Returns alignment of structure neighbors. For comparisons within the PDB, use FSSP. See Structure Searching.
Fold classification based on Structure-Structure alignment of Proteins (FSSP): Returns structural alignments and structurally-based sequence alignments for structure neighbors in the PDB. For structures not in the PDB, see Dali.
Entrez, a powerful system for integrated searching of literature, sequences and genomes, structure, and other databases. See NCBI.
Glossaries include
- Protein Explorer's Help/Index/Glossary (Martz, University of Massachusetts)
- Glossary of Terms from Crystallography, NMR, and Homology Modeling (Rhodes, University of Maine)
- For other bioinformatics glossaries, search Google
HighWire, full-text searching of journal articles.
Journals covering macromolecular structure.
Journal articles on major principles of protein structure.
National Center for Biotechnology Information (NCBI), includes Entrez, PubMed, and a Structure database (see Structure Searching).
OCA, a powerful alternative mechanism for searching the world structure database in the Protein Data Bank.
PDB_Select: generates sequence nonredundant subsets of chains in the Protein Data Bank using methods of Hobohm, Sander et al.. Used by OCA for nonredundant subsets.
Probable Quaternary Structure (PQS) uses an empirically derived weighted score to estimate whether protein-protein contacts that occur in crystals are specific oligomer interfaces or crystal artifacts. For those deemed specific oligomers, the oligomer is provided. When multiple copies of the molecule occur in the asymmetric unit, single copies are provided. PQS also provides complete virus capsids, using symmetry operations typically provided by the authors in the PDB file (virus capsid examples). See PE's Introduction to Probable Quaternary Structure.
Protein Data Bank, the sole primary internationational repository of all published macromolecular 3D structures. Includes extensive links to related bioinformatics resources.
PubMed, searchable journal article abstracts from the US National Library of Medicine. See also HighWire and NCBI.
Structure searching & comparision: finding structure neighbors without reference to sequence: See
- DALI (for unpublished structures)
- Combinatorial Extension.
- FSSP (neighbors within the PDB)
- VAST (Vector Alignment Search Tool) from NCBI.
Structural Classification of Proteins (SCOP). See very brief overview by Chothia et al..
SuMo: Surfing the Molecules. Automated search for similar sites in proteins, "to screen the Protein Data Bank (PDB) for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein. This method is neither based on amino acid sequence nor on fold comparisons. Priority is given to biological relevance." SuMo result for 1LPM (entire protein).
SWISS-MODEL, "an automated comparative protein modelling server". See Introduction to Comparative Modeling.
Swiss-Prot, "a curated protein sequence database which strives to provide a high level of annotations (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."
PISCES: Guoli Wang and Roland Dunbrack's site that culls entries from the PDB based on resolution and sequence identity, among other things. See also PDB_Select.
Visualization Software: See molvisindex.org.
World Index of Molecular Visualization Resources: molvisindex.org. Visitors contribute links to on-line resources in categories including ready to use tutorials on specific molecules (including proteins, organic chemicals, inorganic crystals), K12 resources, resources in German, French, Italian, Japanese, Spanish, etc., technical resources on how to create Chime websites, DeepView (SwissPDB-Viewer) resources, sources of molecules (PDB files), galleries, email lists, free and commercial software. Over 200 entries are described in detail and cross-indexed by subjects and authors.