Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface
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On docking, scoring and assessing protein-DNA complexes in a rigid-body frameworkExtensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers."Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fittingElectrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface designStructure-based modeling of protein: DNA specificity.Atomistic modeling of protein-DNA interaction specificity: progress and applications.Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters.Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking.Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases.Structural analysis of zinc-finger (TTK) + [Cu(BPA)]2+ /[Cu(IDB)]2+ + DNA complexes: an investigation by molecular dynamics simulation.
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P2860
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface
description
article científic
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article scientifique
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articolo scientifico
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artigo científico
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bilimsel makale
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scientific article published on 08 May 2009
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vedecký článok
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vetenskaplig artikel
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videnskabelig artikel
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vědecký článek
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name
Experimentally based contact e ...... aters at the binding interface
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Experimentally based contact e ...... ters at the binding interface.
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type
label
Experimentally based contact e ...... aters at the binding interface
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Experimentally based contact e ...... ters at the binding interface.
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Experimentally based contact e ...... aters at the binding interface
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Experimentally based contact e ...... ters at the binding interface.
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P2860
P356
P1476
Experimentally based contact e ...... aters at the binding interface
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P2093
Carlos J Camacho
N Alpay Temiz
P2860
P304
P356
10.1093/NAR/GKP289
P407
P577
2009-05-08T00:00:00Z