@article {869, title = {DOCKSCORE: a webserver for ranking protein-protein docked poses.}, journal = {BMC Bioinformatics}, volume = {16}, year = {2015}, month = {2015}, pages = {127}, abstract = {

BACKGROUND: Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several reasons such as the large molecular weights of these macromolecular complexes, their dynamic nature, difficulty in purification and sample preparation. Computational docking permits an early understanding of the feasibility and mode of protein-protein interactions. However, docking algorithms propose a number of solutions and it is a challenging task to select the native or near native pose(s) from this pool. DockScore is an objective scoring scheme that can be used to rank protein-protein docked poses. It considers several interface parameters, namely, surface area, evolutionary conservation, hydrophobicity, short contacts and spatial clustering at the interface for scoring.

RESULTS: We have implemented DockScore in form of a webserver for its use by the scientific community. DockScore webserver can be employed, subsequent to docking, to perform scoring of the docked solutions, starting from multiple poses as inputs. The results, on scores and ranks for all the poses, can be downloaded as a csv file and graphical view of the interface of best ranking poses is possible.

CONCLUSIONS: The webserver for DockScore is made freely available for the scientific community at: http://caps.ncbs.res.in/dockscore/ .

}, keywords = {Algorithms, Humans, Internet, Molecular Docking Simulation, Protein Binding, Protein Interaction Domains and Motifs, Proteins, ras GTPase-Activating Proteins, Software}, issn = {1471-2105}, doi = {10.1186/s12859-015-0572-6}, author = {Malhotra, Sony and Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {901, title = {NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.}, journal = {Nucleic Acids Res}, volume = {43}, year = {2015}, month = {2015 Jan}, pages = {D300-5}, abstract = {

NrichD (http://proline.biochem.iisc.ernet.in/NRICHD/) is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural {\textquoteright}intermediately related sequences{\textquoteright} is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been {\textquoteright}enriched{\textquoteright} with these artificial intermediary sequences. NrichD database currently contains 3,611,010 artificial sequences that have been generated between 27,882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

}, keywords = {Computational Biology, Databases, Protein, Internet, Molecular Sequence Annotation, Protein Structure, Tertiary, Sequence Analysis, Protein, Sequence Homology, Amino Acid}, issn = {1362-4962}, doi = {10.1093/nar/gku888}, author = {Mudgal, Richa and Sandhya, Sankaran and Kumar, Gayatri and Sowdhamini, Ramanathan and Chandra, Nagasuma R and Srinivasan, Narayanaswamy} }