(Q47325783)

14 January 2018

title

Weight matrices for protein-DNA binding sites from a single co-crystal structure (English)

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14 January 2018

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Robert G Endres

1

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14 January 2018

Ned S Wingreen

series ordinal

2

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14 January 2018

language of work or name

English

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publication date

28 June 2006

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14 January 2018

published in

Physical Review E

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volume

73

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issue

6 Pt 1

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14 January 2018

page(s)

061921

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14 January 2018

DNA binding sites: representation and discovery

cites work

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.73.061921

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Looking into DNA recognition: zinc finger binding specificity

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Toward an atomistic model for predicting transcription-factor binding sites

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Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

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Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

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Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions

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Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes

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A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA

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Engineering polydactyl zinc-finger transcription factors

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Rotamer libraries in the 21st century

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

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Atomic solvation parameters applied to molecular dynamics of proteins in solution

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Fast accurate evaluation of protein solvent exposure.

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Efficient rotamer elimination applied to protein side-chains and related spin glasses

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Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.

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Sequence logos: a new way to display consensus sequences

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Structural features of protein-nucleic acid recognition sites

21 January 2018

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The role of water in protein-DNA recognition

21 January 2018

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Protein-DNA binding specificity predictions with structural models

21 January 2018

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Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

21 January 2018

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A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

21 January 2018

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The dead-end elimination theorem and its use in protein side-chain positioning

21 January 2018

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Expressing the human genome

21 January 2018

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10.1103/PHYSREVE.73.061921

21 January 2018

Identifiers

DOI

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14 January 2018

ADS bibcode

2006PhRvE..73f1921E

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14 January 2018