iRMSD-APDB statistics

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Protocols

iRMSD-APDB specifications

Information


Unique identifier OMICS_24543
Name iRMSD-APDB
Alternative name iRMSD
Interface Web user interface
Restrictions to use None
Input format CLUSTAL
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Cédric Notredame

Publications for iRMSD-APDB

iRMSD-APDB citations

 (45)
library_books

Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid β

2018
Sci Rep
PMCID: 5913127
PMID: 29686315
DOI: 10.1038/s41598-018-24501-0

[…] . 2000 models were generated for each Fab/Aβ complex, starting from the crystal structure coordinates. Docking plots were then generated using normalized interfaces scores (Isc¯) and interface RMSDs (Irmsd). Discrimination scores were used to quantify the docking performance of the complexes. In brief, docking models were first grouped based on their Irmsd values with cut-offs at ℝ = {1.0, 1.5, 2. […]

library_books

Protein docking refinement by convex underestimation in the low dimensional subspace of encounter complexes

2018
Sci Rep
PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] r better) and High quality solutions before and after SSDU. The classification of the quality of the solutions is based on metrics adopted in the CAPRI experiments. These metrics are: interface RMSD (iRMSD), backbone RMSD (LRMSD) and the number of native contacts preserved (Fnat). To classify a conformation using these metrics, the program DockQ was used. DockQ combines normalized values of iRMSD, […]

library_books

Chikungunya virus nsP1 interacts directly with nsP2 and modulates its ATPase activity

2018
Sci Rep
PMCID: 5773547
PMID: 29348627
DOI: 10.1038/s41598-018-19295-0

[…] on energy. Eelec denotes electrostatic energy term and EDARS refers to the pair wise structure-based potential,. The 1000 lowest energy docked structures are clustered using pair wise interface RMSD (IRMSD) as the distance measure in the second step,. The IRMSD values for each pair among these structures are calculated to determine the structure with highest neighbors within a 9 Å radius. This is […]

library_books

Structure based cross docking analysis of antibody–antigen interactions

2017
Sci Rep
PMCID: 5557897
PMID: 28811664
DOI: 10.1038/s41598-017-08414-y

[…] The cognate and non-cognate models generated by the local refine protocol are typically under 5 Å Cα Irmsd from the native antibody–antigen complexes. That is, model diversity is limited because most model structures have interfaces around the epitope of the antigen. The limited diversity can hinder […]

library_books

Across proteome modeling of dimer structures for the bottom up assembly of protein protein interaction networks

2017
BMC Bioinformatics
PMCID: 5427563
PMID: 28499419
DOI: 10.1186/s12859-017-1675-z

[…] thin the top 10 dimers re-ranked by eRankPPI. Further refinement with FiberDock increases this fraction to as high as 57.5%. In addition to the IS-score, Table  shows that success rates measured with iRMSD as well as PCS increase when eRankPPI and FiberDock are included in the modeling protocol.Fig. 3 Altogether, eRankPPI and FiberDock generate the most accurate dimers in these benchmarking calcu […]

library_books

The pepATTRACT web server for blind, large scale peptide–protein docking

2017
Nucleic Acids Res
PMCID: 5570166
PMID: 28460116
DOI: 10.1093/nar/gkx335

[…] The performance of the rigid-body pepATTRACT web server was tested on the peptiDB benchmark (). For 27/80 complexes, at least one of the 50 models had an interface RMSD (iRMSD) of better than 2 Å. Among the top 10 models, this was achieved for 14 complexes. The full pepATTRACT protocol achieves this for 38 cases, but takes many hours to complete. Thus, increasing the […]

Citations

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iRMSD-APDB institution(s)
Centre For Genomic Regulation (Pompeu Fabra University), Barcelona, Spain; Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, Lausanne University, Lausanne, Switzerland; Department of Computer Science and Industrial Engineering, University of Lleida, Lleida, Spain

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