Publications by authors named "David Beveridge"

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Molecular dynamics of mismatch detection-How MutS uses indirect readout to find errors in DNA.
Abhilash Jayaraj, Kelly M Thayer, David L Beveridge, Manju M Hingorani

Biophys J· August 2023

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Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis.
Benjamin S Cowan, David L Beveridge, Kelly M Thayer

J Phys Chem B· January 2023

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High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants.
Na Le Dang, Anne M Baranger, David L Beveridge

Biomolecules· July 2022

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Estradiol induces allosteric coupling and partitioning of sex-hormone-binding globulin monomers among conformational states.
Ravi Jasuja, Daniel Spencer, Abhilash Jayaraj, Liming Peng, Meenakshi Krishna, David L Beveridge

iScience· June 2021

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Spectral analysis of molecular dynamics simulations on PDZ: MD sectors.
Bharat Lakhani, Kelly M Thayer, Emily Black, David L Beveridge

J Biomol Struct Dyn· February 2020

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Toward a Universal Structural and Energetic Model for Prokaryotic Promoters.
Akhilesh Mishra, Priyanka Siwach, Pallavi Misra, Bhyravabhotla Jayaram, Manju Bansal, David L Beveridge

Biophys J· October 2018

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Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit.
Kelly M Thayer, Bharat Lakhani, David L Beveridge

J Phys Chem B· June 2017

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Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein.
Bharat Lakhani, Kelly M Thayer, Manju M Hingorani, David L Beveridge

J Phys Chem B· March 2017

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Marco Pasi, John H Maddocks, David Beveridge, Thomas C Bishop, David A Case

Nucleic Acids Res· October 2014

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A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes.
Garima Khandelwal, Rebecca A Lee, B Jayaram, David L Beveridge

Biophys J· June 2014

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012.
David L Beveridge, Thomas E Cheatham, Mihaly Mezei

J Biosci· July 2012

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Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.
Surjit B Dixit, Mihaly Mezei, David L Beveridge

J Biosci· July 2012

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U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.
Bethany L Kormos, Susan N Pieniazek, David L Beveridge, Anne M Baranger

Biopolymers· September 2011

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Richard Lavery, Krystyna Zakrzewska, David Beveridge, Thomas C Bishop, David A Case

Nucleic Acids Res· January 2010

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Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
Sobhan Sen, Daniele Andreatta, Sergei Y Ponomarev, David L Beveridge, Mark A Berg

J Am Chem Soc· February 2009

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Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations.
Poonam Singhal, B Jayaram, Surjit B Dixit, David L Beveridge

Biophys J· June 2008

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Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.
Divina Anunciado, Michael Agumeh, Bethany L Kormos, David L Beveridge, Joseph L Knee

J Phys Chem B· May 2008

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CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications.
Weimin Zhong, Surjit B Dixit, Robert J Mallis, Haribabu Arthanari, Alexey A Lugovskoy, David L Beveridge

J Mol Biol· September 2007

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Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model.
Bethany L Kormos, Yulia Benitex, Anne M Baranger, David L Beveridge

J Mol Biol· August 2007

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Identification of an aminoacridine derivative that binds to RNA tetraloops.
Zhaohui Yan, Shweta Sikri, David L Beveridge, Anne M Baranger

J Med Chem· August 2007

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A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.
Bethany L Kormos, Anne M Baranger, David L Beveridge

J Struct Biol· March 2007

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Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex.
Bethany L Kormos, Anne M Baranger, David L Beveridge

J Am Chem Soc· July 2006

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Root mean square deviation probability analysis of molecular dynamics trajectories on DNA.
Surjit B Dixit, Sergei Y Ponomarev, David L Beveridge

J Chem Inf Model· June 2006

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Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction.
Surjit B Dixit, David L Beveridge

Bioinformatics· April 2006

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Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.
Ying Zhao, Bethany L Kormos, David L Beveridge, Anne M Baranger

Biopolymers· March 2006

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