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SBL specifications

Information


Unique identifier OMICS_30959
Name SBL
Alternative name Structural Bioinformatics Library
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
Computer skills Advanced
Version 1.4.0
Stability Stable
Maintained Yes

Subtools


  • FunChaT
  • lRMSD
  • RMSD

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Maintainer


  • person_outline Frederic Cazals <>

Additional information


https://sbl.inria.fr/doc/

Publications for Structural Bioinformatics Library

SBL in publications

 (22)
PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] 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, lrmsd and fnat to generate a continuous score in the range [0,1]; the higher the score, the better the quality of a solution. specifically, a conformation of a protein complex is classified into four […]

PMCID: 5504647
PMID: 28693470
DOI: 10.1186/s12859-017-1733-6

[…] the rosettaligand protocol yielded better results with the classic mc sampling method when using a data set of 100 native protein-ligand complexes. in 71/100 cases, the lowest energy model had an lrmsd less than 2å []. we suggest that the rosettaligand protocol cannot obtain satisfactory results in the remaining cases mainly because the mc sampling technique employed in docking […]

PMCID: 5373608
PMID: 28358834
DOI: 10.1371/journal.pone.0174662

[…] 2 predictions and itscore-pr is better than 3drpc-score and deck-rp when the number of prediction is larger than 3. for difficult cases, all the three scoring functions failed., shows 3drpc-score-lrmsd plots of the decoys of selected rna-protein complexes. among these four rna-protein complexes, 3lwr, 2zue and 3foz are the cases that 3drpc-score successfully pick out the near-native […]

PMCID: 5396268
PMID: 27935158
DOI: 10.1002/prot.25218

[…] interface root mean square deviation (irmsd) and the carbon‐alpha (cα) ligand root mean square deviation (lrmsd). for details of the computation of the fnat and irmsd please see refs. , . the lrmsd is computed by superimposing the receptor chains to their equivalent cα atoms, followed by an lrmsd calculation based on the ligand cα atoms. this lrmsd calculation differs from the standard […]

PMCID: 5001232
PMID: 27535545
DOI: 10.1186/s12864-016-2798-8

[…] querying algorithm in the proposed methodology. the lowest-cost path is computed with a value of max_nn_dist corresponding to about 5.43å /15 (where 5.43å is the least-root-mean-squared-deviation – lrmsd – between the two structures, and 15 relates to the sought path resolution (as described in the “” section. the query is successful; the succession of structures in the path is shown in fig. […]


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SBL institution(s)
Inria, Université Côte d’Azur, Sophia Antipolis, France

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