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Revision as of 12:55, 18 April 2010 (edit) Raghava (Talk | contribs) ← Previous diff		Revision as of 15:53, 19 April 2010 (edit) (undo) Raghava (Talk | contribs) (→Questions we wish to address on PDB file) Next diff →
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	Disordered regions in a protein		Disordered regions in a protein
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		+	Create dataset from PDB_IDs (Sequence, Structure)
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		+	Create non-redundant dataset from CD-HIT , BlastCluster
	[[Category:aminofat]]		[[Category:aminofat]]

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Revision as of 15:53, 19 April 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

Create dataset from PDB_IDs (Sequence, Structure)

Create non-redundant dataset from CD-HIT , BlastCluster