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Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets

R Backofen, S Will, E Bornberg-Bauer
1999 Bioinformatics  
Results: We show how recently developed constraint programming techniques can be used to solve the structure prediction problem efficiently for a higher order alphabet.  ...  Motivation: Predicting the ground state of biopolymers is a notoriously hard problem in biocomputing.  ...  Acknowledgments R.B. and S.W. would like to thank Professor Peter Clote, who got us interested in bioinformatics and inspired this research.  ... 
doi:10.1093/bioinformatics/15.3.234 pmid:10222411 fatcat:i6uhcflkxbdihfeidrpkas266i

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems [chapter]

Michael Stout, Jaume Bacardit, Jonathan D. Hirst, Natalio Krasnogor, Jacek Blazewicz
2006 Lecture Notes in Computer Science  
Predictions using the HP sequence representation with only two residue types were only a little worse than those using a full 20 letter amino acid alphabet (64% vs 68% for two state prediction, 45% vs  ...  That HP sequence information alone can result in predictions accuracies that are within 5% of those obtained using full residue type information indicates that hydrophobicity is a key determinant of CN  ...  In future, we will extend these studies to prediction of other structural attributes, such as secondary structure and relative solvent accessibility.  ... 
doi:10.1007/11732242_19 fatcat:bne4ltzdhbh25kqeghyb2yrxlq

Data Mining in Proteomics with Learning Classifier Systems [chapter]

Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Natalio Krasnogor
2008 Studies in Computational Intelligence  
One such problem, which is one of the fundamental open problems in computational biology is the prediction of the 3D structure of proteins, or protein structure prediction (PSP).  ...  The human experts, with the crucial help of data mining tools, are learning how protein fold to form their structure, but are still far from providing perfect models for all kinds of proteins.  ...  Figure 3 shows a protein sequence represented with the HP alphabet and its optimal structure when using a 3D cubic lattice. Fig. 3 .  ... 
doi:10.1007/978-3-540-78979-6_2 fatcat:skslfyact5cuvni2bfst4xgfde

Protein Structure Prediction with Lattice Models [chapter]

William Hart, Alantha Newman
2005 Chapman & Hall/CRC Computer & Information Science Series  
We also thank Edith Newman for her assistance in creating  ...  as well as an extended HP model on the cubic lattice.  ...  The structures generated by Heun's approximation algorithm on the extended cubic lattice have a similar structure, with 10 hydrophobic columns in the core.  ... 
doi:10.1201/9781420036275.ch30 fatcat:lrwe66yo7zdyjlfvdrhyegv3b4

Approximate protein folding in the HP side chain model on extended cubic lattices

Volker Heun
2003 Discrete Applied Mathematics  
In this paper, we design approximation algorithms for protein structure prediction in the so-called HP side chain model.  ...  To eliminate this drawback, we introduce the extended cubic lattice that extends the cubic lattice by diagonals in the plane.  ...  Algorithm A constructs a folding in the HP side chain model on extended cubic lattices for an arbitrary HP-sequence with an approximation ratio of at least 59=70 (≈ 84:3%).  ... 
doi:10.1016/s0166-218x(02)00382-7 fatcat:2boe2ah5ubdw3l5u553krxr6gi

Comparing folding codes for proteins and polymers

Hue Sun Chan, Ken A. Dill
1996 Proteins: Structure, Function, and Bioinformatics  
Proteins fold to unique compact native structures. Perhaps other polymers could be designed to fold in similar ways.  ...  Adding strong repulsive interactions results in a folding code with more sequences folding uniquely a n d more designable folds.  ...  In the HP model, contacts of type (HH, HP, PP) have energies of (-1~1, 0, 01.'  ... 
doi:10.1002/(sici)1097-0134(199603)24:3<335::aid-prot6>3.0.co;2-f pmid:8778780 fatcat:x5dajq4sg5hyzocdrvipctdh7q

Invariant patterns in crystal lattices: Implications for protein folding algorithms (extended abstract) [chapter]

William E. Hart, Sorin Istrail
1996 Lecture Notes in Computer Science  
Our results are the first in the literature that identify algorithmic paradigms for the protein structure prediction problem that transcend particular lattice formulations.  ...  This paper identifies two classes of invariants, defined in terms of sublattices that are related to the design of algorithms for the structure prediction problem.  ...  Acknowledgements Our thanks to Ken Dill for suggesting the extension of our previous results to other lattice models and for discussions that inspired this work.  ... 
doi:10.1007/3-540-61258-0_21 fatcat:6oa54ikrcnharfhgyngpsgtyci

Automated alphabet reduction method with evolutionary algorithms for protein structure prediction

Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Kumara Sastry, Xavier Llorà, Natalio Krasnogor
2007 Proceedings of the 9th annual conference on Genetic and evolutionary computation - GECCO '07  
This paper focuses on automated procedures to reduce the dimensionality of protein structure prediction datasets by simplifying the way in which the primary sequence of a protein is represented.  ...  Our results show that it is possible to reduce the size of the alphabet used for prediction from twenty to just three letters resulting in more compact, i.e. interpretable, rules.  ...  A recent paper [29] compared the performance of several learning methods applied to predicting the coordination number for lattice-based proteins, real proteins with either HP alphabet or AA alphabet  ... 
doi:10.1145/1276958.1277033 dblp:conf/gecco/BacarditSHSLK07 fatcat:ccuaa7bsxjgghe2arn6hclpjm4

The algorithmics of folding proteins on lattices

Vijay Chandru, Abhi DattaSharma, V.S Anil Kumar
2003 Discrete Applied Mathematics  
Since then, there has been remarkable progress in the algorithmics of folding proteins on discrete lattice models, an account of which is presented herein. ?  ...  The pedagogic cross-disciplinary survey by Ngo, Marks and Karplus (Computational Complexity, Protein Structure Prediction and the Levinthal Paradox, Birkhauser, Basel, 1994) provides an excellent starting  ...  Hart and Istrail [16] extended the original algorithm for the HP model and obtained an approximation factor of 1 12 for the cubic lattice.  ... 
doi:10.1016/s0166-218x(02)00381-5 fatcat:ifisoubuvngwnpvbah5f2fpsdy

Page 2660 of Mathematical Reviews Vol. , Issue 2004c [page]

2004 Mathematical Reviews  
the HP side chain model on extended cubic lattices.  ...  In this paper, we design approx- imation algorithms for protein structure prediction in the so-called HP side chain model.  ... 

EXPLORING PROTEIN'S OPTIMAL HP CONFIGURATIONS BY SELF-ORGANIZING MAPPING

XIANG-SUN ZHANG, YONG WANG, ZHONG-WEI ZHAN, LING-YUN WU, LUONAN CHEN
2005 Journal of Bioinformatics and Computational Biology  
Self-organizing map (SOM) has been used in protein folding prediction when the HP model is employed.  ...  The obtained minimum configuration then has a flexible shape, in contrast to the compact structure limited in the lattice.  ...  In fact, a lattice model with a large alphabet size is effective to increase the prediction accuracy, in contrast to a two-letter HP alphabet, 6 and will be further studied by the SOM algorithm in future  ... 
doi:10.1142/s0219720005001107 pmid:15852511 fatcat:4fxs62w23ja2jeijtwafk3otgy

Multi-Agent Systems Applied In The Modeling And Simulation Of Biological Problems: A Case Study In Protein Folding

Pedro Pablo González Pérez, Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo EduardoSánchez Gutiérrez
2009 Zenodo  
by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice.  ...  in "micro" and "macro" approaches when modeling this type of phenomena.  ...  This type of agent implements the HP model [29, 30] and the extended HPN model.  ... 
doi:10.5281/zenodo.1060185 fatcat:hn2iwf5cora5pf3lharizbogea

The evolutionary landscape of functional model proteins

Jonathan D. Hirst
1999 Protein Engineering Design & Selection  
To study the distinct influences of structure and function on evolution, we propose a minimalist model for proteins with binding pockets, called functional model proteins, based on a shifted-HP model on  ...  These model proteins are not maximally compact and contain an empty lattice site surrounded by at least three nearest neighbors, thus providing a binding pocket.  ...  Despite the predictability of the nature of the binding pocket, we do, in fact, see two types of binding pocket, one with five polar residues and one with six.  ... 
doi:10.1093/protein/12.9.721 pmid:10506281 fatcat:fv7e7ts3r5e4xnk3nebxd4udum

On discrete models and immunological algorithms for protein structure prediction

Vincenzo Cutello, Giuseppe Morelli, Giuseppe Nicosia, Mario Pavone, Giuseppe Scollo
2010 Natural Computing  
Discrete models for protein structure prediction embed the protein amino acid sequence into a discrete spatial structure, usually a lattice, where an optimal tertiary structure is predicted on the basis  ...  While the prediction problem is known to be NP complete even in the simple setting of Dill's model with a 2D-lattice, a variety of bio-inspired algorithms for this problem have been proposed in the literature  ...  to cope with the 2D HP model for the protein structure prediction problem.  ... 
doi:10.1007/s11047-010-9196-y fatcat:ncjnf4vdxnax3bzr6g3ahaxvj4

Comparing Folding Codes in Simple Heteropolymer Models of Protein Evolutionary Landscape: Robustness of the Superfunnel Paradigm

Richard Wroe, Erich Bornberg-Bauer, Hue Sun Chan
2005 Biophysical Journal  
We found that a common practice of restricting protein structure space to maximally compact lattice conformations results in (i.e., "designs in") many encodable (designable) structures that are not otherwise  ...  encodable in the corresponding unrestrained structure space.  ...  The ''hydrophobic polar'' (HP) model (Lau and Dill, 1989; Dill, 1990, 1991; Dill et al., 1995) is a widely used two-letter alphabet (i.e., with two residue or monomer types, H and P).  ... 
doi:10.1529/biophysj.104.050369 pmid:15501948 pmcid:PMC1304991 fatcat:sf23xm7aovhe7dukjpftdqm56m
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