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DOCKSCORE: a webserver for ranking protein-protein docked poses.

Malhotra S, Mathew OK, Sowdhamini R - BMC Bioinformatics (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, India. sonym@ncbs.res.in.

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/ .

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Related in: MedlinePlus

The workflow of the webserver. Input options: User can upload a zipped file containing all the docked poses to be ranked and the coordinate files for both the protein chains. Different parameters which are considered for performing scoring: The user can select the parameters to be used for scoring. For assessing the conservation of interface residues, user can select the parameters for collection of homologs. Main output options: The five top-ranking poses can be visualised with Jmol and the list with the scores can be downloaded in CSV format.
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Related In: Results  -  Collection

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Fig2: The workflow of the webserver. Input options: User can upload a zipped file containing all the docked poses to be ranked and the coordinate files for both the protein chains. Different parameters which are considered for performing scoring: The user can select the parameters to be used for scoring. For assessing the conservation of interface residues, user can select the parameters for collection of homologs. Main output options: The five top-ranking poses can be visualised with Jmol and the list with the scores can be downloaded in CSV format.

Mentions: For performing scoring, the following files should be supplied as an input to the server (FigureĀ 2):Figure 2


DOCKSCORE: a webserver for ranking protein-protein docked poses.

Malhotra S, Mathew OK, Sowdhamini R - BMC Bioinformatics (2015)

The workflow of the webserver. Input options: User can upload a zipped file containing all the docked poses to be ranked and the coordinate files for both the protein chains. Different parameters which are considered for performing scoring: The user can select the parameters to be used for scoring. For assessing the conservation of interface residues, user can select the parameters for collection of homologs. Main output options: The five top-ranking poses can be visualised with Jmol and the list with the scores can be downloaded in CSV format.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4414291&req=5

Fig2: The workflow of the webserver. Input options: User can upload a zipped file containing all the docked poses to be ranked and the coordinate files for both the protein chains. Different parameters which are considered for performing scoring: The user can select the parameters to be used for scoring. For assessing the conservation of interface residues, user can select the parameters for collection of homologs. Main output options: The five top-ranking poses can be visualised with Jmol and the list with the scores can be downloaded in CSV format.
Mentions: For performing scoring, the following files should be supplied as an input to the server (FigureĀ 2):Figure 2

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, India. sonym@ncbs.res.in.

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/ .

Show MeSH
Related in: MedlinePlus