DOCKSCORE: a webserver for ranking protein-protein docked poses

DOCKSCORE: a webserver for ranking protein-protein docked poses

Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different proteinprotein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

Cite us, if you use dockscore
Malhotra S, Mathew O, Sowdhamini R.(2015) DOCKSCORE: a webserver for ranking protein-protein docked poses. BMC Bioinformatics. vol: 16:127. [DOI: 10.1186/s12859-015-0572-6] [PMID: 25902779]


Docked poses: Chain Ids: Chain 1 Chain 2
Upload zip file with poses pdbs Comma Sep. list of Chain ids (max:2) PDB file for the first Chain PDB file for the second Chain

Interface surface area Hydrophobicity Conservation Short Contact Spatial Clustering +vely charged residues

Upload alignment file Chain1 Alignment (.pir) Chain2 Alignment (.pir)
Multiple Sequence alignment file in PIR format for chain 1 Multiple Sequence alignment file in PIR format for chain 2

Evalue Iterations Database Conservation cut-off
Evalue filter for homolog selection No. of PSI blast itemrations Database for homolog search Cut-off value for conservation

MSA Algo. Max. no. of homologues to collect Email:
Algorithm for MSA Number of sequences to be considered for MSA [Optional]To which result shall be sent
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