Structural Biology
General
- Biochemical
Applications of NMR Spectroscopy - Lectures on solution-state nuclear
magnetic resonance techniques (NMR) in biochemistry in PDF format (John Markley,
University of Illinois, Urbana-Champaign)
- Collaborative Computing Project
for NMR - A "public non-profit project serving the macromolecular
NMR community" with software for macromolecular NMR spectroscopy, including
the CcpNmr suite. (University of Camdbridge, UK, and the European Bioinformatics
Institute)
- Interactive
Guide to Diffraction - A "pictorial guide to crystal structures and
their Fourier transforms useful for teaching diffraction physics." (Th.
Proffen and R.B. Neder)
- Macromolecular Crystallography
Links - Links to macromolecular X-ray crystallography sites. (Gerson Cohen,
National Institutes of Health)
- Protein Interaction
Domains - Descriptions of structure and function of major protein interactions
domains (Lab of Tony Pawson, Mount Sinai Hospital, Toronto, Ontario)
- A Protein Primer: A Musical
Introduction to Protein Structure (M.A. Clark, Texas Wesleyan University)
- SBNet - Structural Biology Network
- "The Structural Biology Network, hosted by Uppsala University, unites
academic and industrial structural biologists from the following disciplines:
biomacromolecular X-ray crystallography, high-resolution NMR spectroscopy
of biomacromolecules, near-atomic resolution electron microscopy of biomacromolecules,
computer modelling of biomacromolecules." (Swedish Foundation for Strategic
Research)
- SPR Pages - Information
and links on the use of surface plasmon resonance (SPR) to investigate biomolecular
interactions.
- Wikipedia - Free online encyclopedia
with basic overviews. (Beginner's Level)
See also the Chemical Biology, Enzymes
and Proteins: Biogenesis to Degradation pages.
Macromolecular Structure Databases
- Biological Macromolecule
Crystallization Database (BMCD) - Database that "contains crystal
data and the crystallization conditions, which have been compiled from literature.
[...] [T]he BMCD contains the NASA Protein Crystal Growth Archive, which includes
the crystallization data generated from studies carried out in a microgravity
environment supported by NASA [...] [and] other international space agencies."
(Center for Advanced Research in Biotechnology, National Institute of Standards
and Technology)
- BioMagResBank - Repository for protein,
peptide and nucleic acid NMR data.
- Biomolecules
Gallery - "The Gallery of Biomolecules is an image database which
provides a wide spectrum of high quality pictures of biomolecules such as
nucleic acids, proteins and their complexes." (Kyushu Institute of Technology,
Japan)
- CATH Protein Structure
Classification Database - "CATH is a novel hierarchical classification
of protein domain structures, which clusters proteins at four major levels,
Class (C), Architecture (A), Topology (T) and Homologous superfamily (H)."
(University College London)
- The CMS Molecular Biology Resource
- Links to resources and tools in molecular biology, biotechnology, molecular
evolution, biochemistry and biomolecular modeling. (San Diego Supercomputer
Center)
- Database of Macromolecular Movements
- This site "describes the motions that occur in proteins and other macromolecules,
particularly using movies. Associated with it are a variety of free software
tools and servers for structural analysis." Described in Echols, N.,
Milburn, D. and Gerstein, M. 2003, Nucleic Acids Res. 31:478.
- Database of Simulated
Molecular Motions (DSMM) - "The purpose of this database is to provide
an easily-searchable source of information about movies showing biomolecular
motions that have been generated by computer simulation." Described in
Finocchiaro, G., Wang, T., Hoffmann, R., Gonzalez, A. and Wade, R.C. 2003,
Nucleic Acids Res. 31:456.
- EBI Services - Access
to nucleic acid, protein and macromolecular structure databases, including
the EMBL-Bank database. (European Molecular
Biology Laboratory - European Bioinformatics Institute)
- Entrez - Database
search and retrieval system. (National
Center for Biotechnology Information, National Library of Medicine, National
Institutes of Health)
- ExPASy Proteomics Server - Search protein
databases such as SWISS-PROT, Trembl, PROSITE, ENZYME, etc. (Swiss
Institute of Bioinformatics)
- HOMSTRAD - "HOMSTRAD
(HOMologous STRucture Alignment Database) provides aligned three-dimensional
structures of homologous proteins. The word homology is only used to mean
having a common evolutionary origin, but we practically define homologous
families as a group of proteins with sufficiently high sequence identities.
We combine the classifications proposed by various databases including SCOP,
Pfam, PROSITE and SMART and the results from sequence similarity searches
by PSI-BLAST and FUGUE and make our own decisions to define the families."
(Cambridge University, UK)
- IMB Jena Image Library of Biological
Macromolecules
- ModBase
- Database of protein models (calculated by comparative modeling). (University
of California, San Francisco)
- Polypeptide Ligand Database -
Datavase focused on cystine-knot proteins. (Stanford University)
- Research Collaboratory for Structural
Bioinformatics Protein Data Bank (RSCB PDB) - The largest protein structure
repository and database.
- Structural Classification
of Proteins (SCOP) - Classification of proteins on the basis of structural
motifs.
Structural Biology Software
- PROCHECK
- "Checks the stereochemical quality of a protein structure, producing
a number of PostScript plots analysing its overall and residue-by-residue
geometry."
- RasMol Home Page - Free
software for displaying molecular structures and related resources.
- RCSB PDB Software Links
- - List compiled
by Sierk
and Kleywegt, 2004, Structure, 12:2103-2111.
- Combinatorial Extension (CE)
- Combinatorial extension of fragment alignment, Z-scores; PDB
database. (Shindyalov and Bourne, 1998)
- Distance Matrix Alignment (Dali)
- Distance matrix comparison, Z-scores; FSSP
database. "The Dali server is a network service for comparing protein
structures in 3D. You submit the coordinates of a query protein structure
and Dali compares them against those in the Protein Data Bank." (Holm
and Sander, 1993)
- DEJAVU - For finding structural
motifs in a library; PDB database.
(Kleywegt and Jones, 1997)
- FOLDMINER - SSE alignment;
SCOP database. (Shapiro
and Brutlag, 2004)
- K2SA - Genetic algorithm (Szustakowski
and Weng, 2000)
- LSQMAN - Cα-Cα
distance minimization. (Kleywegt, 1996)
- MAtching Molecular
Models Obtained from THeory (MAMMOTH) - Designed for aligning predicted
structures against the experimental structure. (Ortiz et al., 2002)
- MArkovian TRAnsition
of Structure evolution (MATRAS) - Multi-step algorithm, Z-scores;
SCOP database. (Kawabata
and Nishikawa, 2000)
- PriSM - Hierarchical alignment
method, composite scoring function. (Yang and Honig, 2000)
- ProSup
- Maximize # of aligned residues under a distance threshhold. (Lackner
et al., 2000)
- Structural
Homology by Environment-Based Alignment (SHEBA) - 3D Environment matching.
(Jung and Lee, 2000)
- SSAP
- SSE alignment, dynamic programming; CATH
database. (Orengo and Taylor, 1993)
- Secondary Structure
Matching (SSM) - SSE alignment; PDB
database. (Krissinel and Henrick, 2003)
- Structural Alignment Server
(Structal) - Cα-Cαdistance minimization.
(Levitt and Gerstein, 1998)
- Vector
Alignment Search Tool (VAST) - SSE alignment, P-values; MMDB
database. (Gibrat et al., 1996)
- Structural Biology
Software Database - "This database contains programs which are thought
to be of interest to researchers in the fields of structural biology, quantum
chemistry, and bioinformatics."
- Turbo Frodo - "Turbo
Frodo is a general purpose molecular modelling environnement aimed at people
with the need to model de novo macromolecules, polypeptides as well
as nucleic acids." (Architecture et Fonction des Macromolécules
Biologiques, Centre National de la Recherche Scientifique, France)
See also the Scientific Software page.
Structure and Function Prediction
Servers
- CBS Prediction Servers (Center
for Biological Sequence Analysis, Technical University of Denmark DTU) - Nucleotide
and amino acid sequence-based bioinformatics tools for structure and function
prediction.
- ChloroP - Prediction
of whether or not an amino acid sequence contains an N-terminal chloroplast
transit peptide and probable site for cleavage of the predicted transit
peptide.
- CPHmodels -
Predict protein structure using comparative (homology) modelling.
- DictyOGlyc
- Prediction of GlcNAc O-glycosylation sites in Dictyostelium discoideum
proteins.
- NetOGlycr - Prediction
of mucin type GalNAc O-glycosylation sites in mammalian proteins.
- ProtFun - Prediction
of protein function from sequence.
- SecretomeP
- Prediction of non-classical protein secretion.
- SignalP Server
- Prediction of the presence and location of signal peptide cleavage sites
in amino acid sequences from different organisms: Gram-positive prokaryotes,
Gram-negative prokaryotes, and eukaryotes.
- TargetP - Predictions
of subcellular locations of proteins.
- TMHMM - Prediction
of transmembrane α-helices.
- Finding 3D Similarity - Database and tools
for finding three-dimensional similarities in protein structures.
- Membrane Protein Transmembrane Secondary
Structure Prediction Server
- PhosphoBase -
A database of phosphorylation sites with a phosphorylation prediction program.
- Prediction
of Coiled Coils from Protein Sequences
- PSORT - Prediction of protein
sorting and localization signals.
- WAM - Web Antibody Modelling -
Generation of antibody structure models "based on the AbM package (formerly
marketed by Oxford Molecular) to construct 3D models of antibody Fv sequences
using a combination of established theoretical methods together with the
latest antibody structural information." (Centre for Protein Analysis and
Design, University of Bath, UK)
Discussion Groups
See also the Discussion Groups section
of the General Biochemistry and Cell Biology page.
Labs Studying