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CLIQUE BASED ALGORITHMS FOR PROTEIN THREADING WITH PROFILES AND CONSTRAINTS
2005
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference
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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
2006
IEICE Transactions on Fundamentals of Electronics Communications and Computer Sciences
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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
2003
Genome Informatics Series
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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
2013
Computational biology and chemistry
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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
2018
Briefings in Bioinformatics
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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
2016
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16
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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
2021
Open Journal of Mathematical Optimization
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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]
2020
arXiv
pre-print
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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
2007
Computer journal
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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
2005
Proceedings of the 22nd international conference on Machine learning - ICML '05
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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]
2012
Lecture Notes in Computer Science
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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
2013
Journal of Computational Biology
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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
2006
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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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]
2019
arXiv
pre-print
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2021 accepted doi:10.1002/net.22068 arXiv:1908.00048v2 fatcat:blnqearw4rbutmad33tznnqgby
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
2002
Journal of Molecular Biology
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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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