DonaldJJacobsMD

PubMed

• 1 citations
  Rigidity and flexibility characteristics of DD[E/D]-transposases Mos1 and Sleeping Beauty.
  Christopher M. Singer, Diana Joy, Donald J. Jacobs, Irina V. Nesmelova> ;Proteins. 2019 Apr 1
• Molecular clustering and percolation characteristics near the glass transition in aqueous trehalose and choline dihydrogen phosphate solutions.
  Nikita Nikulsin, E. R. Azhagiya Singam, Gloria D. Elliott, Donald J Jacobs> ;Physical Chemistry Chemical Physics. 2018 Aug 15
• 10 citations
  Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations
  Amit Srivastava, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Dennis R. Livesay, Donald J. Jacobs> ;Biophysical Journal. 2016 May 10
• 12 citations
  Dynamics and thermodynamic properties of CXCL7 chemokine
  Charles A. Herring, Christopher M. Singer, Elena A. Ermakova, Bulat I. Khairutdinov, Yuriy F. Zuev, Donald J. Jacobs, Irina V. Nesmelova> ;Proteins. 2015 Nov 1
• 25 citations
  Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.
  Tong Li, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Donald J. Jacobs, Dennis R. Livesay> ;Plos Computational Biology. 2015 Jul 1
• 28 citations
  Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle
  Tong Li, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Donald J. Jacobs, Dennis R. Livesay> ;Plos One. 2014 Mar 26
• Towards Comprehensive Analysis of Protein Family Quantitative Stability/Flexibility Relationships using Homology Models
  Deeptak Verma, Jun-tao Guo, Donald J. Jacobs, Dennis R. Livesay> ;Methods in Molecular Biology. 2014 Jan 1
• 9 citations
  A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.
  Matthew C. Brown, Deeptak Verma, Christian Russell, Donald J. Jacobs, Dennis R. Livesay> ;Methods in Molecular Biology. 2014 Jan 1
• 508 citations
  Principal component analysis: a method for determining the essential dynamics of proteins.
  Charles David, Donald J. Jacobs> ;Methods in Molecular Biology. 2014 Jan 1
• 19 citations
  Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity.
  Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay> ;Plos Computational Biology. 2013 Jul 18
• 12 citations
  Thermodynamic stability and flexibility characteristics of antibody fragment complexes.
  Tong Li, Deeptak Verma, Malgorzata B. Tracka, Jose Casas-Finet, Dennis R. Livesay, Donald J. Jacobs> ;Protein and Peptide Letters. 2013 Jul 8
• 3 citations
  Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions.
  Shaozhong Deng, Changfeng Xue, Andriy Baumketner, Donald J. Jacobs, Wei Cai> ;Journal of Computational Physics. 2013 Jul 1
• Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.
  Wei Song, Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Wei Cai, Donald J. Jacobs> ;Communications in Computational Physics. 2013 Jan 1
• 3 citations
  ICSM: An order N method for calculating electrostatic interactions added to TINKER
  Katherine Baker, Andrij Baumketner, Yuchun Lin, Shaozhong Deng, Donald J. Jacobs, Wei Cai> ;Computer Physics Communications. 2013 Jan 1
• 23 citations
  Switch II mutants reveal coupling between the nucleotide- and actin-binding regions in myosin V.
  Darshan V. Trivedi, Charles David, Donald J. Jacobs, Christopher M. Yengo> ;Biophysical Journal. 2012 Jun 6
• 34 citations
  Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged
  Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay> ;Plos Computational Biology. 2012 Mar 1
• 6 citations
  Calculating ensemble averaged descriptions of protein rigidity without sampling.
  Luis C. González, Hui Wang, Dennis R. Livesay, Donald J. Jacobs> ;Plos One. 2012 Feb 22
• 14 citations
  Ensemble properties of network rigidity reveal allosteric mechanisms.
  Donald J. Jacobs, Dennis R. Livesay, James M. Mottonen, Oleg Vorov, Andrei Y. Istomin, Deeptak Verma> ;Methods in Molecular Biology. 2012 Jan 1
• 18 citations
  Characterizing protein motions from structure.
  Charles David, Donald J. Jacobs> ;Journal of Molecular Graphics & Modelling. 2011 Nov 1
• 20 citations
  Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle.
  Donald J. Jacobs, Darshan V. Trivedi, Charles David, Christopher M. Yengo> ;Journal of Molecular Biology. 2011 Apr 15
• 4 citations
  Nonadditivity in the alpha-helix to coil transition.
  Gregory G. Wood, Drew A. Clinkenbeard, Donald J. Jacobs> ;Biopolymers. 2011 Apr 1
• 16 citations
  Nonadditivity in Conformational Entropy upon Molecular Rigidification Reveals a Universal Mechanism Affecting Folding Cooperativity
  Oleg Vorov, Dennis R. Livesay, Donald J. Jacobs> ;Biophysical Journal. 2011 Feb 16
• Nonadditivity in the alpha-helix to coil transition.
  Wood, G.G., Clinkenbeard, D.A., Jacobs, D.J.> ;Biopolymers. 2010-12-23
• 2 citations
  A signal processing method to explore similarity in protein flexibility.
  Simina Vasilache, Nazanin Mirshahi, Soo-Yeon Ji, James M. Mottonen, Donald J. Jacobs, Kayvan Najarian> ;Advances in Bioinformatics. 2010 Dec 20
• 14 citations
  Ensemble-based methods for describing protein dynamics
  Donald J. Jacobs> ;Current Opinion in Pharmacology. 2010 Dec 1
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