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Journal of Chemical Information and Modeling|May 23, 2006
Root mean square deviation probability analysis of molecular dynamics trajectories on DNASurjit B Dixit, Sergei Y Ponomarev, David L BeveridgeBioinformatics (Oxford, England)|February 21, 2006
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure predictionSurjit B Dixit, David L BeveridgeJournal of Biosciences|July 4, 2012
Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulationsSurjit B Dixit, Mihaly Mezei, David L BeveridgeProceedings of the National Academy of Sciences of the United States of America|October 7, 2004
Ion motions in molecular dynamics simulations on DNASergei Y Ponomarev, Kelly M Thayer, David L BeveridgeBiophysical Journal|March 11, 2008
Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulationsPoonam Singhal, B Jayaram, Surjit B Dixit, et al.Journal of the American Chemical Society|February 5, 2009
Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experimentsSobhan Sen, Daniele Andreatta, Sergei Y Ponomarev, et al.Journal of Molecular Biology|July 31, 2007
CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implicationsWeimin Zhong, Surjit B Dixit, Robert J Mallis, et al.Proteins|February 22, 2011
Computational prediction and analysis of the DR6-NAPP interactionSergei Y Ponomarev, Joseph AudieJournal of Chemical Theory and Computation|July 12, 2011
Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backboneSergei Y Ponomarev, George A KaminskiJournal of Computer-Aided Molecular Design|December 21, 2005
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src proteinChristophe Chipot, Xavier Rozanska, Surjit B DixitPageof 5