Article

A constraint logic programming approach to 3D structure determination of large protein complexes

Authors: A. Dal Palù, E. Pontelli, J. He, Y. LuAuthors Info & Claims

SAC '06: Proceedings of the 2006 ACM symposium on Applied computing

Pages 131 - 136

Published: 23 April 2006 Publication History

Abstract

The paper describes a novel framework, constructed using constraint logic programming and parallelism, to determine the association between parts of the primary sequence of a protein and α-helices extracted from 3-dimensional low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position, and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

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A. Dal Palu et al. A Constraint Logic Programming Approach to 3D Structure Determination of Large Protein Complexes. NMSU-CS-TR-05., 2005.

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Cited By

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Al Nasr KYousef FJebril RJones C(2018)Analytical Approaches to Improve Accuracy in Solving the Protein Topology ProblemMolecules10.3390/molecules2302002823:2(28)Online publication date: 23-Jan-2018
https://doi.org/10.3390/molecules23020028
Al Nasr KJones CYousef FJebril R(2018) PEM-fitter : A Coarse-Grained Method to Validate Protein Candidate Models Journal of Computational Biology10.1089/cmb.2017.019125:1(21-32)Online publication date: Jan-2018
https://doi.org/10.1089/cmb.2017.0191
Al Nasr KYousef FJones CJebril RHaspel NCowen LShehu AKahveci TPozzi G(2017)Geometry Analysis for Protein Secondary Structures Matching ProblemProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107505(716-721)Online publication date: 20-Aug-2017
https://dl.acm.org/doi/10.1145/3107411.3107505
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Index Terms

A constraint logic programming approach to 3D structure determination of large protein complexes
1. Applied computing
  1. Life and medical sciences

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Published In

SAC '06: Proceedings of the 2006 ACM symposium on Applied computing

April 2006

1967 pages

ISBN:1595931082

DOI:10.1145/1141277

Conference Chair:
Hisham M. Haddad
Kennesaw State University, Kennesaw, Georgia

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

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Published: 23 April 2006

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SIGAPP

SAC06: The 2006 ACM Symposium on Applied Computing

April 23 - 27, 2006

Dijon, France

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Overall Acceptance Rate 1,650 of 6,669 submissions, 25%

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Cited By

View all

Al Nasr KYousef FJebril RJones C(2018)Analytical Approaches to Improve Accuracy in Solving the Protein Topology ProblemMolecules10.3390/molecules2302002823:2(28)Online publication date: 23-Jan-2018
https://doi.org/10.3390/molecules23020028
Al Nasr KJones CYousef FJebril R(2018) PEM-fitter : A Coarse-Grained Method to Validate Protein Candidate Models Journal of Computational Biology10.1089/cmb.2017.019125:1(21-32)Online publication date: Jan-2018
https://doi.org/10.1089/cmb.2017.0191
Al Nasr KYousef FJones CJebril RHaspel NCowen LShehu AKahveci TPozzi G(2017)Geometry Analysis for Protein Secondary Structures Matching ProblemProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107505(716-721)Online publication date: 20-Aug-2017
https://dl.acm.org/doi/10.1145/3107411.3107505
Al Nasr KLiu CRwebangira MBurge LHe J(2013)Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free AlgorithmIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2013.12110:5(1289-1298)Online publication date: 1-Sep-2013
https://dl.acm.org/doi/10.1109/TCBB.2013.121

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A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes

A method for integrative structure determination of protein-protein complexes

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