Web Resources for Bioinformatics Vadim Alexandrov and Mark Gerstein.

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Web Resources for Bioinformatics Vadim Alexandrov and Mark Gerstein

What is Bioinformatics? (Molecular) Bio - informatics One idea for a definition? Bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical- chemistry) and then applying “informatics” techniques (derived from disciplines such as applied math, CS, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Bioinformatics is “MIS” for Molecular Biology Information. It is a practical discipline with many applications.

Web Resources : Molecules –Sequence, Structure, Function Algorithms –HMMs –alignments –simulations Databases

0. Good Starting Point

Web tour of UCL tools and resources

Web tour of UCL tools and resources

1. PDBsum capabilities PDBsum: Starting point for looking at PDB structure Each entry contains: a. View - Schematic pictures of the entry - Interactive views (RasMol/VRML) b. Details - Name, date and description of macromolecules in PDB entry - Authors, resolution and R-factor c. Links - PDB header information - PDB, NDB, SWISSPROT - PQS (protein quaternary structure), MMDB - CATH, SCOP, FSSP - Structure check reports - PROCHECK, WHATIF - Many others – enzyme, PRINTS etc

PDBsum capabilites, continued d. Each chain - CATH classification - Plot of sequence, secondary structure and domain assignments - PROMOTIF analysis - TOPS topology diagram - SAS – annotated FASTA alignment of related sequences in PDB - PROSITE pattern e. Nucleic acid ligands - Base sequence - NUCPLOT diagram of interactions f. Small molecule ligands - Schematic diagram of ligand - LIGPLOT diagram of interactions

2. SAS (Sequence Annotated by Structure): Annotation of protein sequences by structural information. a.Input for FASTA search of rest of PDB -PDB code -SWISS-PROT code -Paste sequence -Upload own alignment b. Annotation -Residue type -Ligand contacts -Active site residues -CATH domains -Residue similarity c. Options -Select inclusion in alignment -Colour/b&w, secondary structure d.View 3D structural superposition -coloured by SAS annotation

3. CATH: Hierarchical domain classification of protein structures in the PDB. Four basic levels: a. Class (automated): secondary structure composition and packing within structure -mainly- , mainly- , mixed , low secondary structure b.Architecture (manual): overall shape of the domain structure as determined by the orientations of the secondary structures. Connectivity is ignored - e.g. barrel, sandwich etc. c.Topology (semi-automated): fold families determined by shape and connectivity of secondary structures -e.g. Mainly-b two-layer sandwich d.Homologous superfamily (semi-automated): domains of common ancestors determined by sequence and structural similarity e.Sequence family (automated): highly similar structures and function as determined by sequence identity

4. Other classification databases a.Enzyme structures database: -PDB enzymes structures classified by E.C. number b.Protein-DNA database: -PDB complex structures classified by binding motif

5. Protein sequence analysis: Protein sequence search using protein fingerprints - group of conserved sequence motifs used to characterize a protein family.

6.Gross-level protein properties Protein-protein interaction server: Protein-DNA interaction server:

7. Atomic-level protein properties a.PROCAT: -Database of 3D enzyme active sites b.Hydrogen bond atlas: -Graphical summary of hydrogen-bonding properties of amino acids c.Atlas of side chain-side chain/side chain-base interactions: -interaction geometries of side chain and side chain-base pairs

8. Publicly available software (protein structure/interaction) a.HBPLUS - calculation of interactions in PDB structures b.LIGPLOT - schematic diagrams of protein-ligand interactions c.NUCPLOT - schematic diagrams of protein-DNA interactions d.PROMOTIF - analyze protein secondary structural motifs e.NACCESS - calculate atomic accessibilities of protein surfaces f.SURFNET - visualization of molecular surfaces, cavities etc g.PROCHECK - check stereochemical quality of protein structures h.THREADER - prediction of protein tertiary structure i.MEMSAT - prediction of transmembrane protein structure j-z BROWSE THE WEB AT YOUR SPARE TIME AND BOOKMARK ‘EM!

‘Domestic’ resources: