Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes (Q33300586)

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English	Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes	scientific article

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scholarly article

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Europe PubMed Central

PubMed publication ID

25 July 2017

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes (English)

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Europe PubMed Central

PubMed publication ID

25 July 2017

Michele Caselle

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Michele Caselle

2

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Federico Fogolari

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Federico Fogolari

3

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author name string

Elisabetta Moroni

1

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Europe PubMed Central

PubMed publication ID

25 July 2017

publication date

27 September 2007

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Europe PubMed Central

PubMed publication ID

25 July 2017

BMC Structural Biology

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Europe PubMed Central

PubMed publication ID

25 July 2017

7

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Europe PubMed Central

PubMed publication ID

25 July 2017

61

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Europe PubMed Central

PubMed publication ID

25 July 2017

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

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21 June 2018

A systems approach to measuring the binding energy landscapes of transcription factors

1 reference

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Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

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Protein-DNA binding specificity predictions with structural models

1 reference

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Ab initio prediction of transcription factor targets using structural knowledge

1 reference

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Ab initio identification of putative human transcription factor binding sites by comparative genomics

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A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes

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Assessing computational tools for the discovery of transcription factor binding sites

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Toward an atomistic model for predicting transcription-factor binding sites

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ConSite: web-based prediction of regulatory elements using cross-species comparison

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WebLogo: A Sequence Logo Generator

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Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs

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Applied bioinformatics for the identification of regulatory elements

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Motif discovery in heterogeneous sequence data.

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Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements

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Identification of conserved regulatory elements by comparative genome analysis

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Discovery of novel transcription factor binding sites by statistical overrepresentation

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Additivity in protein-DNA interactions: how good an approximation is it?

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

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Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

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Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

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cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships

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Genomic strategies to identify mammalian regulatory sequences

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Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA.

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based on heuristic

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10.1186/1472-6807-7-61

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Europe PubMed Central

PubMed publication ID

25 July 2017

1 reference

Dimensions Publication ID

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https://scigraph.springernature.com/pub.10.1186/1472-6807-7-61

9 September 2019

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

25 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

25 July 2017

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