Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions

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dc.catalogadoraba
dc.contributor.authorRibeiro, J.
dc.contributor.authorRíos Vera, C.
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.contributor.authorSchüller, Andreas
dc.date.accessioned2025-02-06T19:08:17Z
dc.date.available2025-02-06T19:08:17Z
dc.date.issued2019
dc.description.abstractSummary Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. Availability and implementation A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. Supplementary information Supplementary data are available at Bioinformatics online.
dc.format.extent3 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1093/bioinformatics/btz062
dc.identifier.eissn1367-4811
dc.identifier.issn1367-4803
dc.identifier.pubmedid30698657
dc.identifier.pubmedidPMC6748739
dc.identifier.scopusid2-s2.0-85072334509
dc.identifier.urihttps://doi.org/10.1093/bioinformatics/btz062
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102172
dc.identifier.wosidWOS:000487327500042
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.information.autorucFacultad de Ciencias Biológicas; Schüller, Andreas; 0000-0002-4443-4279; 207692
dc.issue.numero18
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final3501
dc.pagina.inicio3499
dc.revistaBioinformatics (Oxford, England)
dc.rightsacceso abierto
dc.rights.licenseAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleCalculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
dc.typeartículo
dc.volumen35
sipa.codpersvinculados82342
sipa.codpersvinculados207692
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