Lattice model refinement of protein structures

8 pages•Published: May 15, 2012

Abstract

To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper we formulate and implement a Constraint Programming method to refine such lattice structure models. We show that the approach is able to provide better quality solutions. The prototype is implemented in COLA and is based on limited discrepancy search. Finally, some promising extensions based on local search are discussed.

Keyphrases: lattice models, protein structure prediction

In: Agostino Dovier, Alessandro Dal Palù and Sebastian Will (editors). WCB10. Workshop on Constraint Based Methods for Bioinformatics, vol 4, pages 67-74.

Links:	https://easychair.org/publications/paper/GQK
	https://doi.org/10.29007/c415

BibTeX entry

@inproceedings{WCB10:Lattice_model_refinement_protein,
  author    = {Martin Mann and Alessandro Dal Palù},
  title     = {Lattice model refinement of protein structures},
  booktitle = {WCB10. Workshop on Constraint Based Methods for Bioinformatics},
  editor    = {Agostino Dovier and Alessandro Dal Palù and Sebastian Will},
  series    = {EPiC Series in Computing},
  volume    = {4},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/GQK},
  doi       = {10.29007/c415},
  pages     = {67-74},
  year      = {2012}}

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