Protein Structure Bioinformatics Resources
An arbitrary subset gathered by
provided as a supplement to
EMail suggestions to
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
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-Fun (available from
accepts protein coordinates in the standard PDB format and compares
them with all known protein structures by 3D structural
superposition. Structural hits
having known functions are listed. Thus, 3D-Fun attempts to predict
3D-PSSM, attempts to predict 3D structure
from a protein sequence in part by
known structures and scoring for compatibility.
BioInfoBank Meta Server assists in the construction of
comparative (homology) models.
Integrated access to sequence and structure databases with result
management tools. Very powerful but not very user friendly.
Instructions for use provided in conjunction with Protein Explorer's
- Books on protein structure
Protein Structure Annotation. This meta-server
provides an integrated summary with links to details for
information from the PDB, KEGG, ENZYME, ExPASy, DSSP, CATH, SCOP, SwissProt,
NCBI Taxonomy, GO, and PISCES.
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).
Comparative Modeling (Homology Modeling)
continuously and automatically evaluated by
EVA. There is also a structure prediction meta-server
for difficult cases, the
BioInfoBank Meta Server.
For straightforward cases, comparative modeling is automated by
Predicts possible antigenic epitopes on surfaces of protein antigen
structures submitted. Displays predicted epitopes in Jmol.
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.
Database of Macromolecular Movements:
Categorizes types of movements in conformational changes of macromolecules.
Offers a morph server to animate conformational changes, and an archive
of morphs generated by visitors, with numerous viewing options.
Such morphs can be
animated in Protein Explorer.
a free, powerful molecular modeling program.
Intrinsic Protein Disorder Prediction server.
"DisEMBL is a computational tool for prediction of disordered/unstructured
regions within a protein sequence. ... Avoiding potentially disordered
segments in protein expression constructs can increase expression,
foldability and stability of the expressed protein."
"Database of Protein Disorder (DisProt) is a curated database that provides
information about proteins that lack fixed 3D structure in their putatively
native states, either in their entirety or in part."
Entrez, a powerful
system for integrated searching of literature, sequences and genomes, structure,
and other databases. See NCBI.
continously and automatically analyses protein structure
prediction servers in 'real time'. Evaluates servers for secondary
structure prediction, comparative modeling, inter-residue distances
and contacts, and threading.
Function prediction servers for protein include:
Functional Site prediction servers for protein include:
FSSP: Fold classification based on
Structure-Structure alignment of Proteins:
Returns structural alignments and structurally-based sequence alignments
for structure neighbors in the PDB. For structures not in the PDB,
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
and structure-similarity searching (all under Protein Structure).
searching of journal articles.
Macromolecular Structures, a component of the Sequence Database
HIV Databases at Los Alamos
National Laboratory, Los Alamos, New Mexico USA.
Homology Modeling: see
finds unusual patches on the surface of proteins, and computes just
how unusual they are (patch rareness), and how likely each patch is to
be of functional importance (functional confidence (FC)). The
statistical analysis is done by comparing your protein's surface
against the surfaces and functional sites of a large set of proteins,
with known functional sites."
Journals covering macromolecular structure.
Journal articles on major
principles of protein structure.
predicts "hot spots" in protein-protein interfaces, namely, the
subsets of contacting residues responsible for most of the interfacial
binding free energy.
KFC uses shape specificity, atomic contacts, and noncovalent bond analysis to
to make its predictions.
mutation of hot spots is an effective means of disrupting a protein-protein
interaction. KFC is an alternative to costly experimental identification
of hot spots.
is a server for evaluation of crystallographic models and their agreement with
electron density maps.
It can remove atoms of side chains that are not
consistent with the maps, remove improperly placed water
molecules, check the
B-factors of atoms in the provided model, and compare R and
R-free values obtained as the result of refinement with the
averages characteristic for the data resolution shell.
generates protein backbone and side chain co-ordinates from a C(alpha) trace.
Protein Data Bank
has many membrane-protein specific search capabilities.
- Membrane Protein Structure Databases:
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.
of the molecular model.
National Center for Biotechnology
Information (NCBI), includes
Structure database (see
Most Representative Model: This server identifies the most representative
model in the ensemble of models resulting from NMR experiments.
The most representative model is identified by Olderado (which appeared to
be out of service when this entry was added).
a powerful alternative mechanism for searching the world
structure database in the Protein Data Bank.
Orientations of Proteins in Membranes (OPM)
"provides hydrophobic thicknesses and orientations of membrane
proteins with respect to the hydrocarbon core of the lipid bilayer."
Offers visualization of PDB files with the predicted membrane surface planes
indicated by heteroatoms.
offers a simple interface for searching the World Wide Protein Data
Bank. PDB Lite is designed for students, educators, and non-specialists.
Clear help is provided, crystallographic details are
omitted, and jargon is explained.
PDB_REDO re-refines models from X-ray diffraction
data, sometimes improving the model when compared to the original published
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.
a pictorial database providing an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank.
Includes Jmol view and rotatable (RasMol or Chime) images of surfaces and clefts in surfaces,
and a Raster3D image generating form.
Highlights lists the oldest/newest PDB entries, and those with
the largest/smallest molecules, most chains, longest chains, most/largest
ligands, highest and lowest resolution, etc.
Guoli Wang and Roland Dunbrack's site that
culls entries from the PDB based on resolution and sequence identity,
among other things. See also
PMut: predicts liklihood of disease resulting from mutations
of amino acids in proteins. To display disease-probability as colors
in Chime, go to Precalculated PMut, submit a PDB code (for example,
1IRD for human hemoglobin), and click on the Structure links.
- 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.
calculates vibrational dynamics of protein molecules and among other
things, displays the results as an animation in MDL Chime.
ProSAT: maps ProSite patterns and SWISS-PROT features onto 3D
- Protein Data Bank
primary international repository of all published macromolecular
3D structures. Includes extensive links to related bioinformatics resources.
article abstracts from the US National
Library of Medicine. See also HighWire
- RDP, threading by recursive dynamic programming, available
through the Helmholtz Network
(under Protein Structure).
"A database correlating sequence and atomic coordinate residue
numbering in the Protein Data Bank". Shows alignment of SEQRES
vs. sequence with coordinates in ATOM records. Easiest way to spot
gaps (amino acids in the crystallized compound that lack coordinates),
but doesn't do nucleotides, and does not show sequence microheterogeneity
(updated weekly, fast response; find PDB file, then under Data
Retrieval, click on SEQRES to Coordinates)
Fox Chase Cancer Center
(original development site by Wang and Dunbrack; updated irregularly; slow response).
SPAM: Systematic Protein Annotation
and Modeling is a multi-institutional initiative to
provide tools to assist in selecting and registering
targets for structural genomics and for associating structure with
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
include 123D and
RDP available through the Helmholtz Network
(under Protein Structure), and
Threading servers are continuously and automatically evaluated by
TOPS Services At Glasgow University: Protein topology diagrams,
topology matching between domains, structure comparisons, motif matching.
Transmembrane Protein PDB. Identifies the transmembrane proteins
in the PDB. Searchable, browsable, downloadable.
- Visualization Servers:
These servers assist in generating visualizations
of any model (PDB file) you submit. They require much less technical
knowledge than does direct use of visualization software packages.
- Visualization Software: See molvisindex.org.
WhatIF WWW Interface by Gert Vriend offers some powerful structure validation
and modeling routines, including addition of hydrogens, and
World Index of Molecular Visualization
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.