Protein Structure Bioinformatics Resources
An arbitrary subset gathered by
Eric Martz
provided as a supplement to
Protein Explorer.
EMail suggestions to
me.
*
marks resources linked into Protein Explorer in context-sensitive
help for certain operations, or in the External Resources
window (accessed from the
PE Site Map.
123D+,
threads a sequence through a set of 3D structures. It
combines sequence profiles, secondary structure prediction, and contact capacity potentials
to find the most compatible fold among the 3D structures,
and the best alignment of the sequence with that fold.
3D-PSSM, attempts to predict 3D structure
and probable function from a protein sequence in part by
threading with
known structures and scoring for compatibility.
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.
CASTp:
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.
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.
Entrez, a powerful
system for integrated searching of literature, sequences and genomes, structure,
and other databases. See NCBI.
For other bioinformatics glossaries, search Google
GRASS,
the Graphical Representation and Analysis of Structure Server, using the
widely acclaimed GRASP software, renders a PDB file in a manner
selected by the user from menus, and offers visualization in Chime or VRML as
well as Grasp. Notably, molecular surfaces can be colored by electrostatic
potential, hydrophobicity, distances from a ligand, surface curvature
Helmholtz Network for Bioinformatics:
an integrative web portal for
bioinformatics resources, including protein structure prediction, alignment
generation, threading,
and structure-similarity searching (all under Protein Structure).
HighWire, full-text
searching of journal articles.
MolProbity*
conducts a new and powerful structure validation based on all-atom contacts
analysis, producing automatic corrections (rotamer flips). The flips can be
inspected and accepted or rejected in a java-based Kinemage-style viewer.
The corrected PDB file, containing added hydrogen atoms, is provided.
For secure use, free software that performs the all-atom contacts analysis can be downloaded
and run locally. The server also
offers very useful Ramachandran plots (identifying residues
outside the favorable regions), C-beta deviations, and rotamer analysis.
See
All-Atom Contacts
and
Quality
of the molecular model.
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.
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.
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.
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.
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 structures.
Protein Data Bank*,
the sole
primary international 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.
RDP, threading by recursive dynamic programming, available
through the Helmholtz Network
(under Protein Structure).
STAN:
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.
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-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."
To get Swiss-Prot codes from a PDB code (or EC number), use
PDBSProtEC.
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.