View in EDS

Joint neighbors approximation of macromolecular solvent accessible surface area.

Saved in:
Bibliographic Details
Title: Joint neighbors approximation of macromolecular solvent accessible surface area.
Authors: Rychkov, Georgy, Petukhov, Michael1
Source: Journal of Computational Chemistry. 2007, Vol. 28 Issue 12, p1974-1989. 16p. 3 Diagrams, 5 Charts, 2 Graphs.
Subjects: Approximation theory, Chemical engineering approximation methods, Functional analysis, Macromolecules, Solvents, Atoms, Denaturation of proteins
Abstract: A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 Å2, while for unfolded protein conformations it varies from 1.65 to 1.87 Å2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]
Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
FullText Text:
  Availability: 0
Header DbId: egs
DbLabel: Engineering Source
An: 25541705
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Joint neighbors approximation of macromolecular solvent accessible surface area.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Rychkov%2C+Georgy%22">Rychkov, Georgy</searchLink><br /><searchLink fieldCode="AR" term="%22Petukhov%2C+Michael%22">Petukhov, Michael</searchLink><relatesTo>1</relatesTo>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. 2007, Vol. 28 Issue 12, p1974-1989. 16p. 3 Diagrams, 5 Charts, 2 Graphs.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Approximation+theory%22">Approximation theory</searchLink><br /><searchLink fieldCode="DE" term="%22Chemical+engineering+approximation+methods%22">Chemical engineering approximation methods</searchLink><br /><searchLink fieldCode="DE" term="%22Functional+analysis%22">Functional analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Macromolecules%22">Macromolecules</searchLink><br /><searchLink fieldCode="DE" term="%22Solvents%22">Solvents</searchLink><br /><searchLink fieldCode="DE" term="%22Atoms%22">Atoms</searchLink><br /><searchLink fieldCode="DE" term="%22Denaturation+of+proteins%22">Denaturation of proteins</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 Å2, while for unfolded protein conformations it varies from 1.65 to 1.87 Å2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=25541705
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1002/jcc.20550
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 16
        StartPage: 1974
    Subjects:
      – SubjectFull: Approximation theory
        Type: general
      – SubjectFull: Chemical engineering approximation methods
        Type: general
      – SubjectFull: Functional analysis
        Type: general
      – SubjectFull: Macromolecules
        Type: general
      – SubjectFull: Solvents
        Type: general
      – SubjectFull: Atoms
        Type: general
      – SubjectFull: Denaturation of proteins
        Type: general
    Titles:
      – TitleFull: Joint neighbors approximation of macromolecular solvent accessible surface area.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Rychkov, Georgy
      – PersonEntity:
          Name:
            NameFull: Petukhov, Michael
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 09
              Text: 2007
              Type: published
              Y: 2007
          Identifiers:
            – Type: issn-print
              Value: 01928651
          Numbering:
            – Type: volume
              Value: 28
            – Type: issue
              Value: 12
          Titles:
            – TitleFull: Journal of Computational Chemistry
              Type: main
ResultId 1