Protein Dynamics and Contact Topology Reveal Protein|DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

However, protein dynamics-based attributes could not be found for DNA-binding residues. Interestingly, DNA orientation can be identified by an ' ...

Protein Dynamics and Contact Topology Reveal Protein-DNA ...

Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation. J Chem Theory Comput. 2016 Nov 8;12(11):5269-5277. doi: 10.1021/acs.jctc.

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

We show that protein–DNA docking orientation is a function of protein intrinsic dynamics, but the binding site itself does not display unique patterns.

Protein Dynamics and Contact Topology Reveal Protein-DNA ...

Request PDF | Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation | Structure-encoded conformational dynamics are crucial for ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA Binding Orientation. Aravind Chandrasekaran. ,. Justin Chan. ,. Carmay Lim. ,. Lee Yang 1. Show full ...

Protein dynamics and contact topology reveal protein-DNA binding ...

Protein dynamics and contact topology reveal protein-DNA binding orientation. Authors: Aravind Chandrasekaran · Justin Chan · Carmay Lim · Lee-Wei Yang. Issue ...

Protein Dynamics and Contact Topology Reveal Protein–DNA ...

Protein Dynamics and Contact Topology Reveal Protein–DNA Binding Orientation. J. Chem. Theory Comput. Pub Date : 2016-10-21. DOI : 10.1021/acs.jctc.6b00688.

Protein Dynamics and Contact Topology Reveal ... - ACS Figshare

Save and organize your research references with the Papers cloud library. Access your library anytime, anywhere with the Papers web, desktop, or mobile apps ...

Protein/DNA interactions in complex DNA topologies - NCBI

... dynamics of a closed DNA topology is important. Cryo-electron ... Interplay of protein and DNA structure revealed in simulations of the lac operon ...

Exploring the effect of network topology, mRNA and protein ... - Nature

We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect ...

Exploring Structure, Dynamics, and Topology of Nitroxide Spin ...

... protein secondary and tertiary structure, investigate membrane protein topology, map sequence-specific backbone dynamics, and detect conformational fluctuations ...

Protein folding, protein dynamics and the topology of self-motions

In particular, they show how during folding, the character of the internal motion of a segment can change suddenly and dramatically. They also ...

A topological data analytic approach for discovering biophysical ...

A topological data analytic approach for discovering biophysical signatures in protein dynamics. Wai Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, ...

Topological data analysis of protein structure and inter/intra ...

We created a framework that efficiently utilizes molecular dynamics and persistent homology methods to identify amino acid mutations that induce structural ...

The Topology and Dynamics of Protein Complexes: Insights from Intra

... reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of ...

Long-range correlation in protein dynamics: Confirmation by ... - PLOS

... contact topology defines the slow-mode dynamics of the native proteins. ... proteins show both dense packing and fractal topology. Lastly ...

DNA topology confers sequence specificity to nonspecific ... - PNAS

... protein in wild-type loops attached to the Lac repressor. The computations show how a protein with no discernible DNA sequence-recognizing ...

Topological links in predicted protein complex structures reveal ...

AlphaFold is making great progress in protein structure prediction, not only for single-chain proteins but also for multi-chain protein ...

Mechanistic and thermodynamic characterization of dynamic ...

Mechanistic and thermodynamic characterization of dynamic topology in an unassembled transmembrane protein. ... Together, our results reveal new ...

Professor receives NIH grant to investigate relationship ... - ASU News

... topology and physics-based protein dynamics modeling. The idea comes ... proteins before, but has never combined this data with topological ...