Top PDF Knowledge-based prediction of protein backbone conformation using a structural alphabet
Knowledge-based prediction of protein backbone conformation using a structural alphabet
... most of the previously developed methods for PB prediction except for svmPRAT where it performed ...sets of proteins, an even comparison is hindered by difference in datasets, varying training ...
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Exploring the use of a structural alphabet for a structural prediction of protein loops
... loop conformation prediction ? Our scores are dicult to compare with the results of other approaches, usually in terms of RMS deviations between the predicted conformation - ...
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Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.
... program based on McLachlan algorithm ...only backbone atoms to generate PB sequence and is independent of residues, the user can upload anonymous protein structures by changing all residues to ...
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Structural deformation upon protein-protein interaction: A structural alphabet approach
... The prediction of protein-protein interactions is a current ...ture of the resulting complex, given the structures of inter- acting partners ...performance of ...
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Protein structure analysis, prediction and flexibility in the light of a structural alphabet
... 2fox_: JACKLMMMMMMMMMMMMM Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, de Brevern AG, Offmann B (2006) Protein Block Expert (PBE): a web-based protein structure analysis server ...
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Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.
... is based on the PAPIA/PDB-REPRDB database (Noguchi et ...with a resolution of 2 Å or less and an R-factor less than ...all of the representative chains and a sequence identity no higher ...
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Investigation of the impact of PTMs on the protein backbone conformation
... destabilization) of two other regions, near Thr14-Tyr15, and near Thr39, three other phosphorylation sites related to CDK2 activity and subcellular localization ...the backbone is in agreement with the ...
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mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.
... analysis of function, evolution and architecture of protein ...propose a new web server called mulPBA (multiple Protein Block ...implements a method based on a ...
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SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information
... Results A new structural alphabet encoding: SAFlex Here we propose to extend the SA-based approach, HMM-SA ([ 3 , 15 ]) in SAFlex, to take into account 3D protein flexibility and ...
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Protein structure modeling using backbone chemical shifts
... Refinement of Protein Three-Dimensional Structures and Their ...Modelling of Proteins References The knowledge of the tridimensional structure of a protein is ...
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A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications.
... at a meaningful measurement of the probabilities for short structural motifs to change conformation in topologically equivalent regions is only possible if local backbone of ...
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Protein structure determination using NMR backbone chemical shifts
... University of Liege, Department of chemistry, Structural Biological Chemistry Unit , Liege, 4000, Belgium Introduction The knowledge of the tridimensional structure of a ...
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Local backbone structure prediction of proteins.
... Summary: A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks ...This structural ...
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Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet
... The knowledge of three dimensional structures of proteins gives valuable insights into their ...functions. Prediction of different features of protein structure like ...
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Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight
... potential of a SA-based approach for target flexibil- ity insight, taking into account both sequence and structural ...developed a new tool, referred to as SA-conf, using our ...
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Global analysis of VHHs framework regions with a structural alphabet: VHH FRs structures
... Use of bioinformatics approaches is an essential tool for engineering proteins and a fortiori for ...antibodies. A good knowledge of the sequence – structure relationship, which ...
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Methyl side-chain dynamics prediction based on protein structure
... Thus, prediction of protein conformational flexibility from sequence or structural information has a considerable importance in understanding protein function, and is becoming ...
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Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship
... The knowledge of three dimensional structures of proteins gives valuable insights into their ...functions. Prediction of different features of protein structure like ...
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Protein structure mining using a structural alphabet.
... is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or ...
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Protein short loop prediction in terms of a structural alphabet.
... (887 protein chains, see supplementary material ...importance of sampling. The difference between average and best prediction values is 1% for the prediction rate Q 16 and increases with the ...
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