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Bridging the Protein Sequence-Structure Gap by Structure Predictions

B Rost, C Sander
1996 Annual Review of Biophysics and Biomolecular Structure  
Prediction of protein structure in two dimensions, i.e. prediction of interresidue contacts, is in its infancy.  ...  The problem of accurately predicting protein three-dimensional structure from sequence has yet to be solved.  ...  PREDICTION IN THREE DIMENSIONS Homology Modeling An analysis of the Protein Data Bank (PDB) of experimentally determined structures of protein reveals that all protein pairs with more than 30% pairwise  ... 
doi:10.1146/annurev.bb.25.060196.000553 pmid:8800466 fatcat:mplwauo4q5dtjebkoawq7akyfi

Improving Contact Prediction along Three Dimensions

Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell, Roland L. Dunbrack
2014 PLoS Computational Biology  
Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members.  ...  related proteins; (ii) choose a predictive model to describe a sequence alignment; (iii) infer the model parameters and interpret them in terms of structural properties, such as an accurate contact map  ...  in the dimension of the alignment.  ... 
doi:10.1371/journal.pcbi.1003847 pmid:25299132 pmcid:PMC4191875 fatcat:3fq7jnk6lrgojjdrx4js4z46q4

Dali/FSSP classification of three-dimensional protein folds

L. Holm, C. Sander
1997 Nucleic Acids Research  
For each representative protein chain, there is a database entry containing structure-structure alignments with its structural neighbours in the PDB.  ...  It is derived using an automatic structure comparison program (Dali) for the all-against-all comparison of over 6000 three-dimensional coordinate sets in the Protein Data Bank (PDB).  ...  FSSP entries are parsed on the fly to display selected alignments in one and three dimensions (Fig. 1) .  ... 
doi:10.1093/nar/25.1.231 pmid:9016542 pmcid:PMC146389 fatcat:iwd4ctnuovg2xek2nqubrz35lq

Protein Structure Alignment Using a Graph Matching Technique

Tatsuya Akutsu
1995 Genome Informatics Series  
This paper proposes new algorithms for protein structure alignment. Protein structure alignment is, given two three-dimensional protein structures, to find spatially equivalent residue pairs.  ...  Each algorithm consists of the following two steps: first an initial superposition is computed; then a structure alignment is computed and refined using bipartite graph matching.  ...  Acknowledgement This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas, " Genome Informatics" , from The Ministry of Education, Science, Sports and Culture in Japan  ... 
doi:10.11234/gi1990.6.1 fatcat:tmnuglri4batflaj623orrazae

Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance

Jieping Ye, Ravi Janardan
2004 Journal of Computational Biology  
The algorithm is a heuristic in that it computes an approximation to the optimal multiple structure alignment that minimizes the sum of the pairwise distances between the protein structures.  ...  An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus (pseudo) protein for the set.  ...  ACKNOWLEDGMENTS This effort is sponsored, in part, by the Army High Performance Computing Research Center under the auspices of the Department of the Army, Army Research Laboratory cooperative agreement  ... 
doi:10.1089/cmb.2004.11.986 pmid:15700413 fatcat:silkykml75hrbd67dhybbcvgvq

Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance

Jieping Ye, Ravi Janardan
2004 Journal of Computational Biology  
The algorithm is a heuristic in that it computes an approximation to the optimal multiple structure alignment that minimizes the sum of the pairwise distances between the protein structures.  ...  An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus (pseudo) protein for the set.  ...  ACKNOWLEDGMENTS This effort is sponsored, in part, by the Army High Performance Computing Research Center under the auspices of the Department of the Army, Army Research Laboratory cooperative agreement  ... 
doi:10.1089/1066527042432198 fatcat:sr5dtvcyivgl7lvzbnkl72yypq

Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy of Information

Patrick O'Donoghue, Zaida Luthey-Schulten
2005 Journal of Molecular Biology  
By recasting the problem of redundancy in multiple structural alignments into this framework, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to produce a minimal  ...  We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the  ...  We thank John Eargle for coding the algorithms presented here into a new multiple structural alignment feature in VMD version 1.8.3, 35 and Anurag Sethi for providing the analysis detailed in Figure  ... 
doi:10.1016/j.jmb.2004.11.053 pmid:15713469 fatcat:npfhpniz7fhpbadlf2c4zd5yjm

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments

Ryo Sakai, Jan Aerts
2014 BMC Proceedings  
In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily  ...  It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization.  ...  The aim is to support explorative data analysis at the level of sequence alignment, information theory, and three-dimensional structure.  ... 
doi:10.1186/1753-6561-8-s2-s9 pmid:25237396 pmcid:PMC4155614 fatcat:e2vs4qr5zvgspkr3t6fgn7qxoi

From The Cover: Approximate protein structural alignment in polynomial time

R. Kolodny, N. Linial
2004 Proceedings of the National Academy of Sciences of the United States of America  
Alignment of protein structures is a fundamental task in computational molecular biology.  ...  These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment  ...  In the three dimensions of rotations, the spacing is ␦ r ϭ ͞3c r ; the size of the set in each dimension of rotation is O(c r ͞).  ... 
doi:10.1073/pnas.0404383101 pmid:15304646 pmcid:PMC514457 fatcat:4opegzkwvfba5iwzmjqzcftjey

Better 1D predictions by experts with machines

Burkhard Rost
1997 Proteins: Structure, Function, and Bioinformatics  
Accuracy of predicting protein secondary structure and solvent accessibility has been improved significantly by using evolutionary information contained in multiple sequence alignments.  ...  The fairly accurate predictions of 1D structure were successfully used by various groups for the Asilomar meeting as first step toward predicting higher dimensions of protein structure.  ...  of 1D structure are accurate enough to become a first step in predicting higher dimensions of protein structure (Arthur Lesk, this issue).  ... 
doi:10.1002/(sici)1097-0134(1997)1+<192::aid-prot25>3.0.co;2-i fatcat:4igfmgqblfdkdpuxjh7p7aws3m

Better 1D predictions by experts with machines

Burkhard Rost
1997 Proteins: Structure, Function, and Bioinformatics  
Accuracy of predicting protein secondary structure and solvent accessibility has been improved significantly by using evolutionary information contained in multiple sequence alignments.  ...  The fairly accurate predictions of 1D structure were successfully used by various groups for the Asilomar meeting as first step toward predicting higher dimensions of protein structure.  ...  of 1D structure are accurate enough to become a first step in predicting higher dimensions of protein structure (Arthur Lesk, this issue).  ... 
doi:10.1002/(sici)1097-0134(1997)1+<192::aid-prot25>3.3.co;2-y pmid:9485511 fatcat:w3jraj5cmnh5xiduecaiurb56u

Protein-protein relationship measurement based on relative entropy

Fang-Zhen Li
2012 African Journal of Microbiology Research  
Protein-protein relationship (or evolutionary distance) measurement is an important research topic in phylogenetics. Currently, most of these methods are based on the sequence alignment process.  ...  However, traditional sequence alignment is an NP-hard problem and most algorithms have large scale of computations.  ...  One type of zinc finger is C2H2, for which zinc ion locates in the center of the tetrahedron composed of two Cys and two His.  turn is one of the three basic second structures of proteins, normally consisting  ... 
doi:10.5897/ajmr11.982 fatcat:ubgskyipfnawxgs6t3mpu3opdm

Evolutionary profiles from the QR factorization of multiple sequence alignments

A. Sethi, P. O'Donoghue, Z. Luthey-Schulten
2005 Proceedings of the National Academy of Sciences of the United States of America  
The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear  ...  For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based  ...  The sequence alignment data are encoded in the alignment matrix, A, which is of dimension m ϫ n ϫ d. m is the total length of the multiple alignment, and n is the number of proteins in the alignment.  ... 
doi:10.1073/pnas.0409715102 pmid:15741270 pmcid:PMC554820 fatcat:uf2leqayk5g4hakf5cqekw36gy

Flavitrack analysis of the structure and function of West Nile non-structural proteins

Petr Danecek, Catherine H. Schein
2010 International Journal of Bioinformatics Research and Applications  
Here, PCPMer tools were used to calculate consensus sequences based on conservation of physicochemical properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon  ...  One model structure, based on a nuclear receptor, groups residues essential for West Nile infectivity (I59, V61, and M103) in a pocket on the protein surface.  ...  This enables easy interpretation of large multiple sequence alignments.  ... 
doi:10.1504/ijbra.2010.032117 pmid:20223736 pmcid:PMC2849288 fatcat:mdeenoyko5avpbi2gxlljjik4m

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

M. Errami, C. Geourjon, G. Deleage
2003 Bioinformatics  
Results: We show that the analysis of the secondary structures compatibility is a reliable way to discard nonrelated proteins in low identity multiple alignment.  ...  Motivation: Multiple sequence alignments are essential tools for establishing the homology relations between proteins.  ...  This procedure is performed three times resulting in a first group composed of three alignments.  ... 
doi:10.1093/bioinformatics/btg016 pmid:12611806 fatcat:hd7fohpvwbb45j7mqcwgxz5nua
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