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doi:10.22028/D291-42641
Title: | SphereCon-a method for precise estimation of residue relative solvent accessible area from limited structural information |
Author(s): | Gress, Alexander Kalinina, Olga V. |
Language: | English |
Title: | Bioinformatics |
Volume: | 36 |
Issue: | 11 |
Pages: | 3372-3378 |
Publisher/Platform: | Oxford University Press |
Year of Publication: | 2020 |
DDC notations: | 610 Medicine and health |
Publikation type: | Journal Article |
Abstract: | Motivation: In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results: We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation: https://github.com/kalininalab/spherecon. Contact: alexander.gress@helmholtz-hips.de Supplementary information: Supplementary data are available at Bioinformatics online. |
DOI of the first publication: | 10.1093/bioinformatics/btaa159 |
URL of the first publication: | https://doi.org/10.1093/bioinformatics/btaa159 |
Link to this record: | urn:nbn:de:bsz:291--ds-426418 hdl:20.500.11880/38242 http://dx.doi.org/10.22028/D291-42641 |
ISSN: | 1367-4811 1367-4803 |
Date of registration: | 12-Aug-2024 |
Description of the related object: | Supplementary data |
Related object: | https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/36/11/10.1093_bioinformatics_btaa159/5/bioinformatics_36_11_3372_s5.zip?Expires=1726475347&Signature=LO-A0M2Ir9~xTTa8zAolHyU3v55anDMctVWaLFU9He-n-yxD46uojb5Z-6sgGuVuCYigsS-dTfwTmXldSw-V7G4JcMuUtrzlItsO1uxFwlU4hsIUNdYubGKFASPuyT3yd8doBWMNt9D1IXH4y199XVg5QIKeAHlVABy2VdXWR3zUBGHQ7ZH3gr2jAb4kXpOkGr2l2kaySr75n-QJesF-6SLViAK6ufj7hDKy7Bjrp1fi0OrbrW2bi-HH~fKa6HTxUws-W6XR93jjTG4xhjkiieOV3Kj1wj0EIuY8L-yuOgSl4ZSG2zUnqwVAYJFbZuIh8LDDh0pklryPAkA0Hyn2kw__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA |
Faculty: | M - Medizinische Fakultät |
Department: | M - Medizinische Biometrie, Epidemiologie und medizinische Informatik |
Professorship: | M - Prof. Dr. Olga Kalinina |
Collections: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
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