HARMONY server

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure. Structural descriptors such as backbone conformation, solvent accessibility and hydrogen bonding are used to characterise the structural environment of each residue position. Propensity and Substitution values are used together to predict the occurrence of an amino acid at each position in the sequence on the basis of the local structural environment. We demonstrate that the information from amino acid substitutions among homologous sequences (in the form of environment-dependent amino acid substitution tables) is a powerful tool for identifying errors that may be present in the protein structure.

HARMONY server - Job submission guidelines:

• Please submit single pdb file at a time.
• Please donot submit continous jobs using multiple tabs.
• Please limit your submission to 5 PDB structures per day.

Input methods

1. User may upload structure in PDB format. [Example Run]

2. User may upload alignment file. The alignment should be in PIR. [Example Run]


Upload Structure   [Help]

This option will accept PDB file and search internally for homologues using BLAST and perform multiple alignment.


Upload PDB file :   Example input


Database         NR SwissProt  

Evalue            0.001 0.0001 0.01 0.1 1

Window size   11 21 11 5 2

Upload Structure and Alignment file   [Help]


Upload PDB file :

Upload alignment file :   Example input


Window size   11 21 11 5 2

Contact

Dr.R. Sowdhamini (mini@ncbs.res.in)

Group

Dr.R.Sowdhamini
Dr.N. Srinivasn (ns@mbu.iisc.ernet.in)
G.Pugalenthi
K.Shameer