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." (T. 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)
  • Circular Dichroism
  • Crystallography
  • Mass Spectrometry
  • Nuclear Magnetic Resonance (NMR)
  • Protein Folding
  • Protein Structure
  • Protein Structure Prediction
  • Structural Biology

See also the Chemical Biology, Enzymes and Proteins: Biogenesis to Degradation pages.

Macromolecular Structure Databases

• 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)
• 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)
• 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)."
• Protein
• 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
• 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)
• Polypeptide Ligand Database - Datavase focused on cystine-knot proteins. (Stanford University)
• Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB 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
• Structural Alignment Programs - 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 - C_α-C_α 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)
  • 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) - C_α-C_αdistance 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)

Nucleic Acid, Gene and Genomics Databases

Protein and Proteomics Databases

Discussion Groups

• BioChemWeb.org Discussion Board - Discussions and questions/answers for scientists and students.

• Usenet newsgroup archives from BIOSCI/bionet (can also be accessed through Google Groups: bionet):
  • BIOPHYS/bionet.biophys - The science and profession of biophysics.
  • MOLMODEL/bionet.molec-model - Physical and chemical aspects of molecular modelling.
  • STR-NMR/bionet.structural-nmr - Structural NMR of macromolecules.
  • XTAL-LOG/bionet.xtallography - Discussions about protein crystallography.

See also the Discussion Groups section of the General Biochemistry and Cell Biology page.

Labs Studying Structural Biology