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Structural Alignment
, 2010
"... This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express ..."
Abstract
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This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. JOURNAL OF COGNITION AND DEVELOPMENT, 11(3):356–373 Copyright # 2010 Taylor & Francis Group, LLC ISSN: 1524-8372 print=1532-7647 online
TM-align: A protein structure alignment algorithm based on TM-score
- Nucleic Acids Research
"... TM-score ..."
PROMALS3D: a tool for multiple protein sequence and structure alignments
- Nucleic Acids Res
, 2008
"... structure alignments ..."
Structure–Structure alignment of Proteins
"... Abstract: FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB) (1). The current release has 2860 entries. The FSSP ..."
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Abstract: FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB) (1). The current release has 2860 entries. The FSSP
The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment
- Journal of Computational Biology
, 2005
"... structure alignment ..."
Bayesian protein structure alignment
, 2006
"... The analysis of the three dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins, and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identificati ..."
Abstract
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Cited by 3 (0 self)
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structures; however, all are based on heuristic optimization criteria making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment
Structural alignment of pseudoknotted RNA
- In Proceedings of the Annual Intl. Conference on Computational Biology (RECOMB
, 2006
"... Abstract. In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudo-knotted structures. Our main technical result is an efficient algorithm for computing an optimum structural ..."
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Cited by 5 (2 self)
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structural alignment of an RNA sequence against a genomic substring. This algorithm finds two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our
Twilight Zone of Protein Sequence Alignments
, 1999
"... l findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping Introduction Protein sequence alignments in twilight zone Protein sequences fold into unique three-dimension ..."
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Cited by 397 (49 self)
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l findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping Introduction Protein sequence alignments in twilight zone Protein sequences fold into unique three
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