web resources for bioinformatics vadim alexandrov and mark gerstein
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Web Resourcesfor
Bioinformatics
Vadim Alexandrov and Mark Gerstein
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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.
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Web Resources:
• Molecules– Sequence, Structure,
Function
• Algorithms– HMMs– alignments– simulations
• Databases
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0. Good Starting Point
http://www.ncbi.nlm.nih.gov/
http://www.rcsb.org/pdb/
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Web tour of UCL tools and resources
www.biochem.ucl.ac.uk/bsm/biocomp
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Web tour of UCL tools and resources
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1. PDBsum capabilities PDBsum: www.biochem.ucl.ac.uk/bsm/pdbsumStarting 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
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PDBsum capabilites, continuedd. 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
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2. SAS (Sequence Annotated by Structure): www.biochem.ucl.ac.uk/bsm/sas
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
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3. CATH: www.biochem.ucl.ac.uk/bsm/cathHierarchical 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
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www.biochem.ucl.ac.uk/bsm/cath
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4. Other classification databases
a. Enzyme structures database: www.biochem.ucl.ac.uk/bsm/enzymes
- PDB enzymes structures classified by E.C. number
b. Protein-DNA database: www.biochem.ucl.ac.uk/bsm/prot_dna/prot_dna.html
- PDB complex structures classified by binding motif
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5. Protein sequence analysis: www.biochem.ucl.ac.uk/bsm/dbbrowser
Protein sequence search using
protein fingerprints - group of conserved sequence motifs used to characterize a protein family.
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6. Gross-level protein propertiesProtein-protein interaction server:
www.biochem.ucl.ac.uk/bsm/PP/server
Protein-DNA interaction server:www.biochem.ucl.ac.uk/bsm/PP/server
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7. Atomic-level protein properties
a. PROCAT: www.biochem.ucl.ac.uk/bsm/PROCAT/PROCAT.html
- Database of 3D enzyme active sites
b. Hydrogen bond atlas: www.biochem.ucl.ac.uk/~mcdonald/atlas
- Graphical summary of hydrogen-bonding properties of amino acids
c. Atlas of side chain-side chain/side chain-base interactions:
www.biochem.ucl.ac.uk/bsm/sidechains
- interaction geometries of side chain and side chain-base pairs
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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!
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‘Domestic’ resources: http://bioinfo.mbb.yale.edu/partslist/