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FRODOCK specifications

Information


Unique identifier OMICS_03788
Name FRODOCK
Alternative name Fast Rotational DOCKing
Interface Web user interface
Restrictions to use None
Input data Some 3D coordinates of two interacting proteins.
Input format PDB
Computer skills Basic
Version 2.0
Maintained Yes

Maintainer


  • person_outline Pablo Chacon

Publications for Fast Rotational DOCKing

FRODOCK citations

 (9)
library_books

A novel Gerstmann Sträussler Scheinker disease mutation defines a precursor for amyloidogenic 8 kDa PrP fragments and reveals N terminal structural changes shared by other GSS alleles

2018
PLoS Pathog
PMCID: 5786331
PMID: 29338055
DOI: 10.1371/journal.ppat.1006826

[…] ed in the RPBS Mobyle portal []. 10,000 decoys were created, scored and clustered resulting in 10 models for each of three scoring methods (InterEVScore, SOAP_PP atom-based statistical potential, and FRODOCK). Conservation of residues was assessed with the rate4site. […]

library_books

Structural Analysis of Recombinant Human Preproinsulins by Structure Prediction, Molecular Dynamics, and Protein Protein Docking

2017
PMCID: 5769858
PMID: 29307140
DOI: 10.5808/GI.2017.15.4.142

[…] Protein-protein docking between trypsin (PDB ID: 2PTN) and recombinant proinsulins was performed using the InterEvDock server []. The InterEvDock server provides three kinds of scores: InterEvDock, FRODOCK [], and SOAP_PP []. We chose the SOAP_PP score to evaluate the binding affinities, and docked poses were used to check whether two proteins were bound at the right position. […]

library_books

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

2017
Int J Mol Sci
PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] orm massive numbers of calculations that are run on parallel computing systems, and along with GPU.proton.DOCK and HexServer demonstrates the increase in search speed when using hardware acceleration.FRODOCK projects the interaction terms of a potential protein complex into 3D grid-based potentials using spherical harmonics approximations to accelerate the search; this is itself an extension of th […]

library_books

Applications of contact predictions to structural biology

2017
PMCID: 5414403
PMID: 28512576
DOI: 10.1107/S2052252517005115

[…] t automatically incorporates evolutionary covariance into its calculations has very recently become available (Yu et al., 2016; see Table 1). It carries out rigid-body docking of two structures using FRODOCK (Ramírez-Aportela et al., 2016). A pool of 10 000 poses is then scored in three different fashions, one being a residue-based co-evolution score derived from the i-COMS server (Iserte et al., […]

library_books

DCUN1D3 activates SCFSKP2 ubiquitin E3 ligase activity and cell cycle progression under UV damage

2016
Oncotarget
PMCID: 5295445
PMID: 27542266
DOI: 10.18632/oncotarget.11302

[…] n the HA-CAND1 immunoprecipitates, demonstrating that the two proteins existed as a complex in mammalian cells (Figure ). A sturctural docking model of DCUN1D3-CAND1 interaction was also generated by Frodock 2.0 (J.I. Garzón et al., 2009) in .Furthermore, we sought to examine whether interaction occurs between endogenous DCUN1D3 and CAND1. Endogenous CoIP analysis provided evidence for the endogen […]

library_books

A STIM2 splice variant negatively regulates store operated calcium entry

2015
Nat Commun
PMCID: 4411291
PMID: 25896806
DOI: 10.1038/ncomms7899

[…] ible loop (model 2) or a partial helix (models 3 and 4). Upon docking these dimer models of the STIM CAD domains to the Orai1 C-terminal helix using the three different docking packages DOT2 (ref. ), FRODOCK and ZDOCK, this extension turned out to have a significant, consistent impact on the predicted Orai1-binding sites. For the STIM1 CAD dimer, all best-scoring solutions generated by the package […]

Citations

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FRODOCK institution(s)
Department of Biological Chemical Physics, Chinaasolano Physical Chemistry Institute CSIC, Madrid, Spain; Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
FRODOCK funding source(s)
Supported by Spanish grants BFU2013-44306-P, and BFU2014-51823-R from the Ministerio de Economıa y Competitividad (MINECO) and CM S2010/BMD-2353 from the Comunidad de Madrid.

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