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Links tagged with 'protein subunits'

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Protein Peeling 3 DTool Content

http://www.dsimb.inserm.fr/dsimb_tools/peeling3/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structural Features

Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
Protein Peeling 3D: new tools for analyzing protein structures20111
Protein Peeling 2: a web server to convert protein structures into series of protein units200610
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments200615
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence chemical models computer simulation molecular models molecular sequence data peptide fragments peptide mapping protein conformation protein folding protein sequence analysis protein subunits proteins statistical models tertiary protein structure

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition200628
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition200487
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding200262
Structure-based prediction of DNA target sites by regulatory proteins1999141
NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

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