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 in publications

 (36)
PMCID: 5913127
PMID: 29686315
DOI: 10.1038/s41598-018-24501-0

[…] the normalized rosetta interface scores (in reu). the x-axis shows the deviation of the docking model from the starting crystal structure of the complex using rmsd of the fab/aβ interface residues (irmsd). we quantified the docking performance of the fab/aβ complexes using a discrimination score. discrimination score captures the favorability of the interface scores of the near-native docking […]

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

[…] 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 […]

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

[…] 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. […]

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

[…] due to the inaccuracies in the backbone conformations in unbound and homology models.table 2 , 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 […]

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

[…] than 0.210, 0.311 and 0.473 indicating a statistically significant interface similarity at p-values of 10-2, 10-5 and 10-10, respectively. in addition, the quality of dimer models is assessed with irmsd, a standard evaluation measure in the critical assessment of predicted interactions (capri) [] and the pairwise contact score (pcs) []. irmsd is the interfacial cα-rmsd between ligands […]


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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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