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." (T.
Proffen and R.B. Neder)
Protein Interaction
Domains - Descriptions of structure and function of major protein interactions
domains (Lab of Tony Pawson, Mount Sinai Hospital, Toronto, Ontario)
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)
Biological Macromolecule
Crystallization Database (BMCB) - 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)
CMS Molecular Biology Resource - Links to resources and tools in molecular biology, biotechnology, molecular
evolution, biochemistry and biomolecular modeling.
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.
Structure - "The
NCBI Structure Group maintains MMDB,
a database of macromolecular 3D structures, as well as tools for their
visualization and comparative analysis. MMDB, the Molecular Modeling
Database, contains experimentally determined biopolymer structures obtained
from the Protein
Data Bank (PDB)."
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)
Math-for-Health
Sample Decomp Output - "This corporate site contains a freely accessible
database of more than 1000 structurally decomposed and automatically repaired
PDB files, with precisely identified protein-ligand complexes." (Math-for-Health)
ModBase - Database of protein models (calculated by comparative modeling). (University
of California, San Francisco)
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.
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)
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)
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.
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)
