AminoFAT
From DrugPedia: A Wikipedia for Drug discovery
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[http://bip.weizmann.ac.il/oca-bin/lpccsu/ LPC]: Ligan protein contact prediction | [http://bip.weizmann.ac.il/oca-bin/lpccsu/ LPC]: Ligan protein contact prediction | ||
| - | + | [http://bioinformatics.charite.de/supersite SuperSite]: dictionary of metabolite and drug binding sites in proteins | |
== Questions we wish to address on PDB file == | == Questions we wish to address on PDB file == | ||
Revision as of 19:01, 27 March 2010
AminoFAT: Functional Annotation of Amino Acids
This page maintain software or databases important for predicting functional properties of amino acids in a protein.
Important Software
DSSP: For assigning secondary structure of proteins from PDB
pdb-tools: A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files
HBPLUS: is a hydrogen bond calculation program
NACCESS: A program for calculating accessible area
PDBsum: Summary of protein
LPC: Ligan protein contact prediction
SuperSite: dictionary of metabolite and drug binding sites in proteins
Questions we wish to address on PDB file
Assigning secondary structure in a PDB file using dssp
Assigning turns in PDB
PDB have highest/lowest composition of a particular residue type
PDB files having highest/lowest types of residues (charged, polar, hydrophobicity) RNA interacting residues
DNA interacting residues
Protein/peptides interacting residues
Protein-small molecules interaction
Protein-carbohydrate interacting residues
Post translation modification
Disordered regions in a protein
