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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.
The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete setExpand
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B-DNA twisting correlates with base-pair morphology.
The observed sequence dependence of the mean twist angles in 38 B-DNA crystal structures can be understood in terms of simple geometrical features of the constituent base-pairs. Structures with lowExpand
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DNA stretching and compression: large-scale simulations of double helical structures.
Computer-simulated elongation and compression of A - and B -DNA structures beyond the range of thermal fluctuations provide new insights into high energy "activated" forms of DNA implicated inExpand
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Hybrid parallel tempering and simulated annealing method
In this paper, we propose a new hybrid scheme of parallel tempering and simulated annealing (hybrid PT/SA) with an efficient barrier-crossing capability. Expand
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Architectural Accommodation in the Complex of Four p53 DNA Binding Domain Peptides with the p21/waf1/cip1 DNA Response Element*
High resolution chemical footprinting and cross-linking experiments have provided a basis for elucidating the overall architecture of the complex between the core DNA binding domain of p53 (p53DBD,Expand
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Static and statistical bending of DNA evaluated by Monte Carlo simulations.
To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5.T5 and A4.T4 blocks. Monte Carlo simulations haveExpand
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Bending of DNA by asymmetric charge neutralization: all-atom energy simulations.
DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have beenExpand
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Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A.
A growing body of evidence suggests a connection between protein dynamics and enzymatic catalysis. In this paper, we present a variety of computational studies designed to investigate the role ofExpand
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Protein docking using surface matching and supervised machine learning
Computational prediction of protein complex structures through docking offers a means to gain a mechanistic understanding of protein interactions that mediate biological processes. This isExpand
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Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar proteins together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and combining these scores for each PDB entry in order to predict the complex structure. Expand
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