From DrugPedia: A Wikipedia for Drug discovery

Revision as of 17:25, 26 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

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