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CLIQUE BASED ALGORITHMS FOR PROTEIN THREADING WITH PROFILES AND CONSTRAINTS

K.C. DUKKA BAHADUR, ETSUJI TOMITA, JUN'ICHI SUZUKI, KATSUHISA HORIMOTO, TATSUYA AKUTSU
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
problem with profiles and constraints.  ...  Protein threading with profiles in which constraints on distances between residues are given is known to be NP-hard.  ...  In this regard, we had also reported a mathematical analysis of protein threading with profiles and constraints and presented practical algorithms for protein threading with profiles and constraints.  ... 
doi:10.1142/9781860947322_0006 fatcat:znfkibvkerhb7mjag6sx7sw5ba

Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints

T. AKUTSU
2006 IEICE Transactions on Fundamentals of Electronics Communications and Computer Sciences  
In this paper, we consider a variant of the protein threading problem with profiles in which constraints on distances between residues are given.  ...  The protein threading problem with profiles is known to be efficiently solvable using dynamic programming.  ...  Acknowledgements This work was supported in part by Grants-in-Aid #17017019 and #16300092 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, and by the Kayamori Foundation  ... 
doi:10.1093/ietfec/e89-a.5.1215 fatcat:ovbmtrr6s5aj3iykrlj57rfojy

Algorithms for Computing an Optimal Protein Threading with Profiles and Distance Restraints

Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto
2003 Genome Informatics Series  
Though Xu et al. considered protein threading with pairwise contact energy and constraints [5], threading with profiles is also known as a powerful method for protein structure prediction.  ...  Therefore, we have recently developed two algorithms for computing optimal threadings with profiles and constraints [1] . In this short abstract, we show performances of these two algorithms.  ... 
doi:10.11234/gi1990.14.480 fatcat:zseaejnu6fharayhra3p3hyhhq

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment

Ryan Day, Hyun Joo, Archana C. Chavan, Kristin P. Lennox, Y. Ann Chen, David B. Dahl, Marina Vannucci, Jerry W. Tsai
2013 Computational biology and chemistry  
Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets.  ...  As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed.  ...  Acknowledgment This work is funded by the National Institutes of Health grants R01GM81631 and R01GM104972.  ... 
doi:10.1016/j.compbiolchem.2012.10.008 pmid:23266765 pmcid:PMC3867305 fatcat:pqsbwre6qrdengs6q6hyl4gkju

Binding site matching in rational drug design: algorithms and applications

Misagh Naderi, Jeffrey Mitchell Lemoine, Rajiv Gandhi Govindaraj, Omar Zade Kana, Wei Pan Feinstein, Michal Brylinski
2018 Briefings in Bioinformatics  
In this review, we survey 12 tools widely used to match pockets. These methods are divided into five categories based on the algorithm implemented to construct binding-site alignments.  ...  In addition to the comprehensive analysis of their algorithms, test sets and the performance of each method are described.  ...  SMAP defines a profile distance based on the amino acid frequency, which is used as a weight associated with the newly merged graph vertices.  ... 
doi:10.1093/bib/bby078 pmid:30169563 fatcat:csn3azed2bhlfacmrpb7ad7oea

A Multithreaded Algorithm for Mining Maximal Cohesive Dense Modules from Interaction Networks with Gene Profiles

Aditya Goparaju, Saeed Salem
2016 Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16  
For relaxed constraints the number of result clusters on a large graph can be very high and we need a way to find a representative set of clusters which can be most similar to all remaining clusters.  ...  Experiments on two real interaction networks show the effectiveness of the proposed algorithm.  ...  Hence our definition of distance is based on the similarity in the network structure and the relevant attributes.  ... 
doi:10.1145/2975167.2985693 dblp:conf/bcb/GoparajuS16 fatcat:dpvocluh4vba3giafxkewd7w2y

The Referenced Vertex Ordering Problem: Theory, Applications, and Solution Methods

Jérémy Omer, Antonio Mucherino
2021 Open Journal of Mathematical Optimization  
Our implementation of the branch-and-bound algorithm, together with all instances we have used, is publicly available on GitLab 1 .  ...  We then discuss how upper and lower bounds can be computed during the enumeration to design a branch-and-bound algorithm.  ...  In this section the reader can find the corresponding performance profiles: developed by Dolan and Moré [6] , performance profiles allow us to scale the execution times of the compared algorithms with  ... 
doi:10.5802/ojmo.8 fatcat:vuxhfdzq2jhyjhzbt2jp4bwqea

Integer Programming, Constraint Programming, and Hybrid Decomposition Approaches to Discretizable Distance Geometry Problems [article]

Moira MacNeil, Merve Bodur
2020 arXiv   pre-print
We propose an integer programming formulation and three constraint programming formulations that all significantly outperform the state-of-the-art cutting plane algorithm for this problem.  ...  Given an integer dimension K and a simple, undirected graph G with positive edge weights, the Distance Geometry Problem (DGP) aims to find a realization function mapping each vertex to a coordinate in  ...  Acknowledgments We are grateful to Leo Liberti for introducing us to the distance geometry area and this particular topic.  ... 
arXiv:1907.12468v3 fatcat:h5mi75au4bdmvdrolkfc7to5ti

Parameterized Complexity and Biopolymer Sequence Comparison

L. Cai, X. Huang, C. Liu, F. Rosamond, Y. Song
2007 Computer journal  
The article surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence, pairwise  ...  Algorithm techniques built on the structural-unit level, as well as on the residue level, are discussed.  ...  Tree-decomposition based algorithms and protein threading Tree decomposition based methods have been successful in threading.  ... 
doi:10.1093/comjnl/bxm035 fatcat:nycuqgahm5fibhrwhoqjw4tcke

Predicting protein folds with structural repeats using a chain graph model

Yan Liu, Eric P. Xing, Jaime Carbonell
2005 Proceedings of the 22nd international conference on Machine learning - ICML '05  
However, extant approaches often perform inadequately due to their inability to capture longrange interactions between structural units and to handle low sequence similarities across proteins (under 25%  ...  Protein fold recognition is a key step towards inferring the tertiary structures from amino-acid sequences.  ...  Acknowledgments This material is based upon work supported by the National Science Foundation under Grant No. 0225656 and Pennsylvania TSF grant.  ... 
doi:10.1145/1102351.1102416 dblp:conf/icml/LiuXC05 fatcat:lhkvg6g2rzebroqnvlybdlvukm

Ballast: A Ball-Based Algorithm for Structural Motifs [chapter]

Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg
2012 Lecture Notes in Computer Science  
However, it remains an open problem as to how best to leverage the local geometric and chemical constraints underlying structural motifs in order to develop motif-finding algorithms that are both theoretically  ...  We present a simple, general, efficient approach, called Ballast (Ball-based algorithm for structural motifs), to match given structural motifs to given structures.  ...  A document with full proofs and additional results is available at www.cs.dartmouth.edu/~cbk/ballast/recomb12-suppl.pdf. A Java implementation of Ballast is freely available upon request.  ... 
doi:10.1007/978-3-642-29627-7_9 fatcat:nwieccv7dfbt5de5t3x44zlziq

Ballast: A Ball-based Algorithm for Structural Motifs

Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg
2013 Journal of Computational Biology  
However, it remains an open problem as to how best to leverage the local geometric and chemical constraints underlying structural motifs in order to develop motif-finding algorithms that are both theoretically  ...  We present a simple, general, efficient approach, called Ballast (Ball-based algorithm for structural motifs), to match given structural motifs to given structures.  ...  A document with full proofs and additional results is available at www.cs.dartmouth.edu/~cbk/ballast/recomb12-suppl.pdf. A Java implementation of Ballast is freely available upon request.  ... 
doi:10.1089/cmb.2012.0246 pmid:23383999 pmcid:PMC3576911 fatcat:lbf6zq6y3zbc5jnwey7hodzz74

Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment

Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell Malmberg, Ying Xu, Liming Cai
2006 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
This paper demonstrates a successful application of the algorithm to RNA structure search used for noncoding RNA identification. An application to protein threading is also discussed.  ...  Index Terms-Structure-sequence alignment, tree decomposition, parameterized algorithm, dynamic programming, RNA structure homology search, protein threading.  ...  A detailed discussion is given to show how an efficient algorithm for protein threading can be constructed based on the introduced alignment algorithm and related techniques.  ... 
doi:10.1109/tcbb.2006.52 pmid:17085850 fatcat:jj3vma4ue5hzrnw6qltquvsgda

Constraint Programming Approaches to the Discretizable Molecular Distance Geometry Problem [article]

Moira MacNeil, Merve Bodur
2019 arXiv   pre-print
We propose the first constraint programming formulations as well as a set of checks for proving infeasibility, domain reduction techniques, symmetry breaking constraints and valid inequalities.  ...  The Distance Geometry Problem (DGP) seeks to find positions for a set of points in geometric space when some distances between pairs of these points are known.  ...  Acknowledgements We are grateful to Leo Liberti for introducing us to the area of distance geometry and this topic in particular.  ... 
arXiv:1908.00048v1 fatcat:e7ims76jg5g6tkdmlzeleu57yq

Quantifying the Similarities within Fold Space

Andrew Harrison, Frances Pearl, Richard Mott, Janet Thornton, Christine Orengo
2002 Journal of Molecular Biology  
We have used GRATH, a graph-based structure comparison algorithm, to map the similarities between the different folds observed in the CATH domain structure database.  ...  However, in other regions of fold space much more discrete topologies are observed with little similarity between folds. Abbreviations used: CASP, competitive assessment of structure prediction.  ...  related to our use of graph theory; Ian Longden, Andreas Brakoulias & David Gilbert for discussions about aspects of algorithms and improving the efficiency of GRATH; all the members of the CATH team  ... 
doi:10.1016/s0022-2836(02)00992-0 pmid:12417203 fatcat:wnybwphkrjg63gvmnlvtfwf2nu
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