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Results 1 - 10
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14,030
Hidden Markov models for detecting remote protein homologies
- Bioinformatics
, 1998
"... A new hidden Markov model method (SAM-T98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAM-T98 is ..."
Abstract
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Cited by 462 (15 self)
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A new hidden Markov model method (SAM-T98) for nding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (hmm) from the sequence and homologs found using the hmm for database search. SAM-T98
The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling
- BIOINFORMATICS
, 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all re ..."
Abstract
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Cited by 575 (5 self)
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Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all
Low-homology protein threading
- Bioinformatics 2010
"... Motivation: The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method ..."
Abstract
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Cited by 9 (1 self)
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HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases. Results: We present a profile-entropy dependent scoring function
Protein homology detection by HMM-HMM comparison
- BIOINFORMATICS
, 2005
"... Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile H ..."
Abstract
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Cited by 401 (8 self)
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Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile
CATH -- a hierarchic classification of protein domain structures
- STRUCTURE
, 1997
"... Background: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can ..."
Abstract
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Cited by 470 (33 self)
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classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast
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 ..."
Abstract
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Cited by 397 (49 self)
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alignments have uncovered homologous protein pairs with less than 10% pairwise sequence identity (
Modeling structurally variable regions in homologous proteins with rosetta
- Proteins
, 2004
"... ABSTRACT A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because structural differences between homologous proteins are responsible for variations in protein function and ..."
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Cited by 53 (12 self)
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ABSTRACT A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because structural differences between homologous proteins are responsible for variations in protein function
Results 1 - 10
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14,030
