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Protein Domain Identification and Improved Sequence Similarity
and the optimization of structural prediction methods.8. The correct ... on inferring domains by searching sequence databases,16 –19 mainly based on fast .... until domain assignment ends and no new homologues are found any- more.
[ george_heringa_psfg_48_672_681_2002.pdf - Read/Download File

Rapid protein domain assignment from amino acid sequence using
Keywords: Domains; secondary structure; protein folding; sequence analysis; structure prediction. Since the first protein ... termined structure and searching the target sequence against sequence domain databases results in a lack of significant matches. In such ... structure prediction accuracy (Jones 1999) where methods.
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Sequence-based prediction of protein domains - Nucleic Acids
Jul 7, 2004 ... ous domain assignment methods and databases have been developed for proteins of ... align the secondary structure predicted for a query protein against a ... below). We obtained multiple sequence alignments by search-.
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Meta-DP: domain prediction meta-server - Bioinformatics
simple interface to predict domains in a given protein sequence using a number of ... Moreover, database searching, phylogeny and protein modeling often perform better ..... (1998) Domain assignment for protein structures using a consensus.
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Protein Domain Prediction Using Profiles, Secondary Structure
Keywords: protein structure prediction, domain, recursive neural networks. 1. ... The final assignment of protein domains is the result of ... database contains only the sequences of domain regions, sequences from the. Protein Data ..... (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search.
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Statistical Methods for Protein Structure Prediction
Protein Sequence. Database Searching. Domain Assignment. Multiple Sequence . Alignment. Homologue in PDB. Comparative. Modelling. Secondary. Structure.
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CATH – a hierarchic classification of protein domain structures
A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure–function/ evolution relationships to both .... were added to these families by searching for significantly high structural similarity and ..... of sequence-structure relationships thereby improving structure prediction ...
[ 1-s2.0-S0969212697002608-main.pdf?_tid=9f25fcd8-2744-11e4-b520-00000aab0f27&acdnat=1408413821_af59520905c892fcfce4e64747b7b416 - Read/Download File

FFAS03: a server for profile–profile sequence alignments - CiteSeerX
The most effective methods of protein structure and function ... The fold and function assignment system (FFAS) is a ... FFAS03 server allows searching of five databases of protein ... algorithms for protein domain prediction, such as DomPred.
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A computational strategy for protein function assignment - NCBI
between short signals and functional annotations in a protein database is presented. ... a certain keyword is only assigned to a sequence if sequence similarity is found in the position described ... Searching for .... all of the known protein structural domains orga- nized in a ... as a query to predict its function or structure, such.
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SUPERFAMILY: HMMs representing all proteins of known structure
alignments and genome assignments ... genomics, gene prediction and domain- based genomic studies. ... to search sequence databases for homologues.
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Fast assignment of protein structures to sequences using the
... the sequences of the domains of proteins of known structure as the query se- .... For structural assignment, this .... search programs on PDB-ISL, a database with sequences ..... Yuan,Y. and Bork,P. (1998) Homology-based fold predictions for.
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Protein fold recognition from secondary structure assignments
being a domain from the E. coli bio protein known to adopt an SH2 ... to secondary structure prediction accuracy, through the use of ... ture assignments available for proteins prior to 3D structure ... prediction from multiple sequence alignment require several quite .... and restraints is used to search a database of pro-. 303.
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MODBASE, a database of annotated comparative protein structure
models for domains in 304 517 out of 539 171 unique protein sequences ... TrEMBL (5) and GenPept (6) protein sequence databases. ... protein structure prediction methods, including threading and ... functional sites by 3D motif searching, determining structure ... fold assignment and establishing evolutionary relationships.
[ Pieper_NucleicAcidsRes_2002.pdf - Read/Download File

Assignment of Homology to Genome Sequences - Bad Request
ing HMMs for sequences of proteins of known structure. For a family of ... Introduction. Protein structure prediction, to discover the fold ... here are the protein domains as classi®ed by. SCOP. ... search of a large non-redundant protein database.
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Advances in structural genomics - MRC Laboratory of Molecular
a new perspective on domain structures, gene duplications, protein families and ... assignment of three-dimensional structures to the protein products of ... matched to the sequences of proteins of known structure ... logucs of the query in a sequence database and then builds a profile of ... domain sequences to MG proteins.
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The Natural History of Protein Domains - Annual Reviews
Key Words protein evolution, protein structure, sequence analysis, domain classification ... THE ROLE OF DOMAINS IN PREDICTING FUNCTION . ... course it is central to methods of domain assignment based on sequence similarity, ..... sensitivity of sequence and structure database searching algorithms improves, the.
[ annurev.biophys.31.082901.134314 - Read/Download File

9 Understanding Tools and Techniques in Protein Structure Prediction
Sep 12, 2011 ... and prediction by database search; sequence alignment; secondary structure prediction; motifs ... to deposition of protein structures in the public domain. An identity of ..... domain identification and fold assignment). Fig. 6.
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Automated Prediction of CASP-5 Structures Using the Robetta Server
Key words: automated protein structure prediction server; CASP .... Carlo conformational search procedure.8 ..... sequence, assignment of domains to the appropriate proto- col, and .... are selected from a database of known structures using.
[ proteins.53_524-33.pdf - Read/Download File

A comparative proteomics resource: proteins of Arabidopsis thaliana
Jul 28, 2003 ... functional domain assignment, we analyzed all the proteins of Arabidopsis thaliana. Three- ... (NCBI) maintains a Conserved Domain Database (CDD) that. Published: 28 ... ity search; PEDANT is a comprehensive analysis pipeline .... Domain location prediction by sequence. Structure. Sequence. Step 1.
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Domain boundary prediction based on profile domain linker
domain proteins but also for the experimental structure determination. In this work , a novel ... tate (Wen et al., 2005), database searching (Nikitin and Lisacek,. 2003), protein ... forward way to predict domains was by sequence homology or multiple .... There are many methods of domain assignment for pro- tein structures: ...
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