Automated bond order assignment as an optimization problem
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Anna Katharina Dehof
- Alexander Rurainski
- Quang Bao Anh Bui
- Sebastian Boecker
- Hans-Peter Lenhof
- Andreas Hildebrandt
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000287758400004&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/bioinformatics/btq718
- eISSN
- 1460-2059
- Externe Identifier
- Clarivate Analytics Document Solution ID: 726WU
- PubMed Identifier: 21245051
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- BIOINFORMATICS
- Paginierung
- 619 - 625
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Titel
- Automated bond order assignment as an optimization problem
- Sub types
- Article
- Ausgabe der Zeitschrift
- 27
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Abstract
- <jats:title>Abstract</jats:title> <jats:p>Motivation: Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach.</jats:p> <jats:p>Results: We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods.</jats:p> <jats:p>Availability: The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.</jats:p> <jats:p>Contact: anna.dehof@bioinf.uni-sb.de</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p>
- Autoren
- Anna Katharina Dehof
- Alexander Rurainski
- Quang Bao Anh Bui
- Sebastian Böcker
- Hans-Peter Lenhof
- Andreas Hildebrandt
- DOI
- 10.1093/bioinformatics/btq718
- eISSN
- 1367-4811
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- Bioinformatics
- Sprache
- en
- Online publication date
- 2011
- Paginierung
- 619 - 625
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/bioinformatics/btq718
- Datum der Datenerfassung
- 2023
- Titel
- Automated bond order assignment as an optimization problem
- Ausgabe der Zeitschrift
- 27
Data source: Crossref
- Abstract
- <h4>Motivation</h4>Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach.<h4>Results</h4>We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods.<h4>Availability</h4>The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.
- Addresses
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany. anna.dehof@bioinf.uni-sb.de
- Autoren
- Anna Katharina Dehof
- Alexander Rurainski
- Quang Bao Anh Bui
- Sebastian Böcker
- Hans-Peter Lenhof
- Andreas Hildebrandt
- DOI
- 10.1093/bioinformatics/btq718
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Identifier: 21245051
- Open access
- false
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- Bioinformatics (Oxford, England)
- Schlüsselwörter
- Proteins
- Nucleic Acids
- Ligands
- Linear Models
- Computational Biology
- Molecular Conformation
- Hydrogen Bonding
- Algorithms
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2011
- Paginierung
- 619 - 625
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Datum der Datenerfassung
- 2011
- Titel
- Automated bond order assignment as an optimization problem.
- Sub types
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 27
Data source: Europe PubMed Central
- Abstract
- MOTIVATION: Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach. RESULTS: We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods. AVAILABILITY: The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.
- Autoren
- Anna Katharina Dehof
- Alexander Rurainski
- Quang Bao Anh Bui
- Sebastian Böcker
- Hans-Peter Lenhof
- Andreas Hildebrandt
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/21245051
- DOI
- 10.1093/bioinformatics/btq718
- eISSN
- 1367-4811
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- Bioinformatics
- Schlüsselwörter
- Algorithms
- Computational Biology
- Hydrogen Bonding
- Ligands
- Linear Models
- Molecular Conformation
- Nucleic Acids
- Proteins
- Sprache
- eng
- Country
- England
- Paginierung
- 619 - 625
- PII
- btq718
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2011
- Titel
- Automated bond order assignment as an optimization problem.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 27
Data source: PubMed
- Autoren
- Anna Katharina Dehof
- Alexander Rurainski
- Quang Bao Anh Bui
- Sebastian Böcker
- Hans-Peter Lenhof
- Andreas Hildebrandt
- Zeitschrift
- Bioinformatics
- Artikelnummer
- 5
- Paginierung
- 619 - 625
- Datum der Veröffentlichung
- 2011
- Herausgeber
- Oxford Univ Press
- Datum der Datenerfassung
- 2020
- Titel
- Automated bond order assignment as an optimization problem
- Sub types
- article
- Ausgabe der Zeitschrift
- 27
Data source: Manual
- Beziehungen:
- Property of