From DrugPedia: A Wikipedia for Drug discovery

Revision as of 09:40, 17 September 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 (Installed)

SuperSite: dictionary of metabolite and drug binding sites in proteins

PDBcat: Simple program to read columns (Installed)

SMSD: Small Molecule Subgraph Detector

PDBFINDER2 : Combines PDB, DSSP, HSSP

JOElib: open source computational chemistry package written in Java

• • FPOCKET : Fpocket: An open source platform for ligand pocket detection

TMACC: Topological Maximum Cross Correlation descriptors

PerlMol: Perl Modules for Molecular Chemistry

ParsePDB: A Perl Parser for PDB Files

MOPAC: Molecular Orbital PACkage

PDBselect creating non-redundant datasets

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

Create dataset from PDB_IDs (Sequence, Structure)

Create non-redundant dataset from CD-HIT , BlastCluster

More about your PDBid (Like link to PDB, PDBwiki, Topsan, protopedia)

Extract PDBids from PDB which satisfy particular criteria (R < 2.5, X-ray, ATP binder, GTP binder)

Filter PDBids supplied by user which satisfy particular condition

Database of D-amino acids