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A Constraint Programming Approach for Structural Bioinformatics Problems
January 2007
BaKr07
In this paper we show how Constraint Programming (CP) techniques have been used to handle bioinformatics structural problems, namely in protein structure prediction and protein interaction (docking). Solving these problems requires innovative modelling of the problem variables and constraints, and the application of advanced CP features to handle the problems efficiently, namely the exploitation of global constraints and local search, in addition to more standard binary constraint propagation. Both applications, respectively PSICO (Processing Structural Information with Constraint programming and Optimisation), and BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) have been incorporated in a platform, Chemera, that aims at supporting (and has effectively supported, namely in protein docking), biochemists in their research.
In proceedings
Pedro Barahona, Ludwig Krippahl
Michael Hanus
9th International Symposium on Practical Aspects of Declarative Languages
Lecture Notes in Computer Science
Springer
Nice, France
4354
33 - 49
978-3-540-69608-7
0302-9743
-
-
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Pedro Barahona and Ludwig Krippahl, A Constraint Programming Approach for Structural Bioinformatics Problems, in: Michael Hanus (eds), 9th International Symposium on Practical Aspects of Declarative Languages, Lecture Notes in Computer Science, Springer, Nice, France, Vol. 4354, ISBN 978-3-540-69608-7, ISSN 0302-9743, Pag. 33 - 49, January 2007.
<a href="/people/members/view.php?code=7e27bc13fad97e99cd21ea6914d55659" class="author">Pedro Barahona</a> and <a href="/people/members/view.php?code=195d68ea5904b58472fd8c8aedcae233" class="author">Ludwig Krippahl</a>, <b>A Constraint Programming Approach for Structural Bioinformatics Problems</b>, in: Michael Hanus (eds), <u>9th International Symposium on Practical Aspects of Declarative Languages</u>, Lecture Notes in Computer Science, <a href="http://www.springer.com" title="Link to external entity..." target="_blank" class="publisher">Springer</a>, Nice, France, Vol. 4354, ISBN 978-3-540-69608-7, ISSN 0302-9743, Pag. 33 - 49, January 2007.
@inproceedings {BaKr07, author = {Pedro Barahona and Ludwig Krippahl}, editor = {Michael Hanus}, title = {A Constraint Programming Approach for Structural Bioinformatics Problems}, booktitle = {9th International Symposium on Practical Aspects of Declarative Languages}, series = {Lecture Notes in Computer Science}, publisher = {Springer}, address = {Nice, France}, volume = {4354}, pages = {33 - 49}, isbn = {978-3-540-69608-7}, issn = {0302-9743}, abstract = {In this paper we show how Constraint Programming (CP) techniques have been used to handle bioinformatics structural problems, namely in protein structure prediction and protein interaction (docking). Solving these problems requires innovative modelling of the problem variables and constraints, and the application of advanced CP features to handle the problems efficiently, namely the exploitation of global constraints and local search, in addition to more standard binary constraint propagation. Both applications, respectively PSICO (Processing Structural Information with Constraint programming and Optimisation), and BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) have been incorporated in a platform, Chemera, that aims at supporting (and has effectively supported, namely in protein docking), biochemists in their research.}, month = {January}, year = {2007}, }
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