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DOCKSCORE specifications

Information


Unique identifier OMICS_08208
Name DOCKSCORE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ramanathan Sowdhamini

Information


Unique identifier OMICS_08208
Name DOCKSCORE
Interface Web user interface
Restrictions to use None
Programming languages Java, Javascript, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ramanathan Sowdhamini

Publication for DOCKSCORE

DOCKSCORE citations

 (22)
library_books

Control of leucine dependent mTORC1 pathway through chemical intervention of leucyl tRNA synthetase and RagD interaction

2017
Nat Commun
PMCID: 5622079
PMID: 28963468
DOI: 10.1038/s41467-017-00785-0

[…] a shape comparison filter is combined with a Monte Carlo conformational search for generating ligand poses consistent with the active site shape. The top 10 conformations were generated based on the DockScore value after the energy minimization using smart minimizer method. The docked poses were then analyzed using the scoring functions, including Dock scores, LigScore1 and LigScore2, PLP1 and PL […]

call_split

Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β TrCP

2017
Sci Rep
PMCID: 5514133
PMID: 28717195
DOI: 10.1038/s41598-017-05944-3
call_split See protocol

[…] using Autodock Vina. During molecular docking the receptor molecule remained rigid while the peptides were treated as flexible. All of the obtained peptides conformations were evaluated based on Vina DockScore, RMSD calculations and the interaction energy with the help of Sybyl8.1 software. The binding energy calculations were performed based on the individual free energy values of peptides, recep […]

call_split

Integrative modelling of TIR domain containing adaptor molecule inducing interferon β (TRIF) provides insights into its autoinhibited state

2017
Biol Direct
PMCID: 5397763
PMID: 28427457
DOI: 10.1186/s13062-017-0179-0
call_split See protocol

[…] , using the acidic residues lining the major cleft of N-terminal domain to guide the docking, the top poses were those in which the BB loop was present in the interface Docked poses were ranked using DockScore [] and interactions at the interface identified using PPCheck []. Both these softwares were developed in the lab. DockScore is a scoring scheme that utilizes various parameters such as the n […]

library_books

In silico Approach for Anti Thrombosis Drug Discovery: P2Y1R Structure Based TCMs Screening

2017
Front Pharmacol
PMCID: 5220089
PMID: 28119608
DOI: 10.3389/fphar.2016.00531

[…] multi-conformational compound molecular structures were generated using Monte Carlo algorithm-based conformational analysis and rigid body minimization completed using the Smart Minimizer module. The DockScore was adopted as the LigandFit scoring to rank the TCMSP compounds that docked into the P2Y1R ligand-binding pocket for MRS2500. The LigandFit docking procedure consists of the following two s […]

library_books

Understanding the diverse functions of Huatan Tongluo Fang on rheumatoid arthritis from a pharmacological perspective

2016
PMCID: 4906768
PMID: 27347021
DOI: 10.3892/etm.2016.3329

[…] hydrogen atoms were added. An inhibitor from the PDB file was used to define the active site. HTTLF compounds were docked onto the protein models. The interactions between these were evaluated using DockScore (). The compounds with the top 20 DockScores were selected as potentially active compounds of HTTLF (). […]

library_books

Deciphering the underlying mechanisms of Diesun Miaofang in traumatic injury from a systems pharmacology perspective

2015
PMCID: 4464322
PMID: 25891262
DOI: 10.3892/mmr.2015.3638

[…] n atoms were added. The inhibitor from the crystal structure defined the active site. A total of 158 DSMF compounds were docked into the protein models and interactions between them were evaluated by DockScore which estimates the ligand position and orientation based on the most favorable energy production from the interactions between the ligand conformations and receptor proteins (). Compounds w […]

Citations

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DOCKSCORE institution(s)
National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bangalore, India

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