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Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
Proteins, structure, function, and bioinformatics, 2003, Vol.53 (S6), p.430-435
Petrey, Donald
Xiang, Zhexin
Tang, Christopher L.
Xie, Lei
Gimpelev, Marina
Mitros, Therese
Soto, Cinque S.
Goldsmith-Fischman, Sharon
Kernytsky, Andrew
Schlessinger, Avner
Koh, Ingrid Y.Y.
Alexov, Emil
Honig, Barry
2003
Details
Autor(en) / Beteiligte
Petrey, Donald
Xiang, Zhexin
Tang, Christopher L.
Xie, Lei
Gimpelev, Marina
Mitros, Therese
Soto, Cinque S.
Goldsmith-Fischman, Sharon
Kernytsky, Andrew
Schlessinger, Avner
Koh, Ingrid Y.Y.
Alexov, Emil
Honig, Barry
Titel
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
Ist Teil von
Proteins, structure, function, and bioinformatics, 2003, Vol.53 (S6), p.430-435
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2003
Link zum Volltext
Quelle
Wiley Online Library - AutoHoldings Journals
Beschreibungen/Notizen
We participated in the fold recognition and homology sections of CASP5 using primarily in‐house software. The central feature of our structure prediction strategy involved the ability to generate good sequence‐to‐structure alignments and to quickly transform them into models that could be evaluated both with energy‐based methods and manually. The in‐house tools we used include: a) HMAP (Hybrid Multidimensional Alignment Profile)—a profile‐to‐profile alignment method that is derived from sequence‐enhanced multiple structure alignments in core regions, and sequence motifs in non‐structurally conserved regions. b) NEST–a fast model building program that applies an “artificial evolution” algorithm to construct a model from a given template and alignment. c) GRASP2–a new structure and alignment visualization program incorporating multiple structure superposition and domain database scanning modules. These methods were combined with model evaluation based on all atom and simplified physical‐chemical energy functions. All of these methods were under development during CASP5 and consequently a great deal of manual analysis was carried out at each stage of the prediction process. This interactive model building procedure has several advantages and suggests important ways in which our and other methods can be improved, examples of which are provided. Proteins 2003;53:430–435. © 2003 Wiley‐Liss, Inc.
Sprache
Englisch
Identifikatoren
ISSN: 0887-3585
eISSN: 1097-0134
DOI: 10.1002/prot.10550
Titel-ID: cdi_proquest_miscellaneous_71342629
Format
–
Schlagworte
Algorithms
,
Amino Acid Sequence
,
Binding Sites - genetics
,
fold recognition
,
homology modeling
,
Models, Molecular
,
Molecular Sequence Data
,
profile-profile alignment
,
Protein Folding
,
protein structure alignment
,
Protein Structure, Tertiary
,
Proteins - chemistry
,
Proteins - genetics
,
Sequence Alignment - methods
,
Sequence Homology, Amino Acid
,
Thermodynamics
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