A filtering technique for fragment assembly- based proteins loop modeling with constraints

Federico Campeotto, Alessandro Dal Palù, Agostino Dovier, Ferdinando Fioretto, Enrico Pontelli

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Methods to predict the structure of a protein often rely on the knowledge of macro sub-structures and their exact or approximated relative positions in space. The parts connecting these sub-structures are called loops and, in general, they are characterized by a high degree of freedom. The modeling of loops is a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a class of constraints that models a general multi-body system; we present a proof of NP-completeness and provide filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations. The paper shows the application of the constraint in solving the protein loop modeling problem, based on fragments assembly.

Original languageEnglish (US)
Title of host publicationPrinciples and Practice of Constraint Programming - 18th International Conference, CP 2012, Proceedings
Pages850-866
Number of pages17
DOIs
StatePublished - Nov 7 2012
Externally publishedYes
Event18th International Conference on Principles and Practice of Constraint Programming, CP 2012 - Quebec City, QC, Canada
Duration: Oct 8 2012Oct 12 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7514 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference18th International Conference on Principles and Practice of Constraint Programming, CP 2012
CountryCanada
CityQuebec City, QC
Period10/8/1210/12/12

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Campeotto, F., Dal Palù, A., Dovier, A., Fioretto, F., & Pontelli, E. (2012). A filtering technique for fragment assembly- based proteins loop modeling with constraints. In Principles and Practice of Constraint Programming - 18th International Conference, CP 2012, Proceedings (pp. 850-866). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7514 LNCS). https://doi.org/10.1007/978-3-642-33558-7_61