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dc.contributor.authorRuvinsky, Anatoly M.
dc.contributor.authorVakser, Ilya A.
dc.date.accessioned2015-04-09T17:23:23Z
dc.date.available2015-04-09T17:23:23Z
dc.date.issued2008-09-01
dc.identifier.citationRuvinsky, Anatoly M. & Vakser, Ilya A. "Chasing funnels on protein-protein energy landscapes at different resolutions." Biophysical Journal. Volume 95, Issue 5, 1 September 2008, Pages 2150–2159. http://dx.doi.org/10.1529/biophysj.108.132977.en_US
dc.identifier.urihttp://hdl.handle.net/1808/17369
dc.descriptionThis is the published version, also available here: http://dx.doi.org/10.1529/biophysj.108.132977.en_US
dc.description.abstractStudies of intermolecular energy landscapes are important for understanding protein association and adequate modeling of protein interactions. Landscape representation at different resolutions can be used for the refinement of docking predictions and detection of macro characteristics, like the binding funnel. A representative set of protein-protein complexes was used to systematically map the intermolecular landscape by grid-based docking. The change of the resolution was achieved by varying the range of the potential, according to the variable resolution GRAMM methodology. A formalism was developed to consistently parameterize the potential and describe essential characteristics of the landscape. The results of gradual landscape smoothing, from high to low resolution, indicate that i), the number of energy basins, the landscape ruggedness, and the slope decrease accordingly; ii), the number of near-native matches, defined as those inside the funnel, increases until the trend breaks down at critical resolution; the rate of the increase and the critical resolution are specific to the type of a complex (enzyme inhibitor, antigen-antibody, and other), reflect known underlying recognition factors, and correlate with earlier determined estimates of the funnel size; iii), the native/nonnative energy gap, a major characteristic of the energy minima hierarchy, remains constant; and iv), the putative funnel (defined as the deepest basin) has the largest average depth-related ruggedness and slope, at all resolutions. The results facilitate better understanding of the binding landscapes and suggest directions for implementation in practical docking protocols.en_US
dc.publisherBiophysical Societyen_US
dc.titleChasing Funnels on Protein-Protein Energy Landscapes at Different Resolutionsen_US
dc.typeArticle
kusw.kuauthorVakser, Ilya A.
kusw.kudepartmentMolecular Biosciencesen_US
dc.identifier.doi10.1529/biophysj.108.132977
kusw.oaversionScholarly/refereed, publisher version
kusw.oapolicyThis item meets KU Open Access policy criteria.
dc.rights.accessrightsopenAccess


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