Protein Structure Bioinformatics Resources
An arbitrary subset gathered by
provided as a supplement to
EMail suggestions to
- Books on protein structure
Critical Assessment of PRedicted Interactions,
to assess the capacity of protein-protein
docking methods to predict protein-protein
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.
Ten Most Wanted,
to provide structural and functional insights into biologically important
proteins, particularly those that are intractable to experimental structural
A server that identifies pockets and cavities in proteins, and quantitates
their volumes. Atoms lining each pocket or cavity can be displayed in Chime,
RasMol, or MAGE.
- Cavities and pockets in proteins, see
Finding 3D similarities in protein structures without reference
to sequence. Automated intelligent alignment of protein chains
(ligands are discarded).
Automated identification of functional regions in proteins of known
3D structure based upon evolutionary conservation.
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
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,
Entrez, a powerful
system for integrated searching of literature, sequences and genomes, structure,
and other databases. See NCBI.
searching of journal articles.
Journals covering macromolecular structure.
Journal articles on major
principles of protein structure.
National Center for Biotechnology
Information (NCBI), includes
Structure database (see
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.
PDBSProtEC: A resource to link PDB chains with SwissProt codes and EC
numbers. Enter one of a PDB identification code, an EC (Enzyme
Commission) number, or a Swiss-Prot identification code(s), and get the other
two. Updated daily.
- Pockets and cavities in proteins, see
- 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
PQS also provides complete virus capsids,
using symmetry operations typically provided by the authors in the
(virus capsid examples).
See PE's Introduction to Probable Quaternary
PROCAT, a database where you can search for 3D enzyme active site template
motifs in a protein structure.
ProSAT: maps ProSite patterns and SWISS-PROT features onto 3D
- 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
STructure ANalysis server at University of Uppsala, Sweden. Includes
Ramachandran analysis and
routines to detect water molecules that should be metal cations,
and trans peptides that should be cis.
Structure searching & comparision: finding structure neighbors
without reference to sequence: See
Structural Classification of Proteins (SCOP).
See very brief overview by
Chothia et al..
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
SuMo result for 1LPM (entire protein).
"an automated comparative protein modelling server".
See Introduction to Comparative Modeling.
"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."
To get Swiss-Prot codes from a PDB code (or EC number), use
Guoli Wang and Roland Dunbrack's site that
culls entries from the PDB based on resolution and sequence identity,
among other things. See also
TOPS Services At Glasgow University: Protein topology diagrams,
topology matching between domains, structure comparisons, motif matching.
- 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.