Rutgers Main | CIRC | Quantitative Biology   
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Darrin M. York

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

DOI: 10.1021/acs.jctc.7b00102 Download PDF

Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

DOI: 10.1002/anie.201705608 Download PDF

Quantum mechanical force fields for condensed phase molecular simulations'

J. Phys.: Condens. Matter, (2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c Download PDF

Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

Biochemistry, (2017) 56, 2985-2994
DOI: 10.1021/acs.biochem.6b01192 Download PDF

Creation of Academic Social Networks (ASNs) for Effective Online eLearning Communities

DOI: 10.1021/bk-2016-1217.ch009

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

RNA, (2016) 22, 32-48
DOI: 10.1261/rna.053710.115 Download PDF

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

J. Comput. Aided Mol. Des., (2016) 30, 533-539
DOI: 10.1007/s10822-016-9920-5 Download PDF

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Acta Crystallogr. D Struct Biol., (2016) 72, 1062-1072
DOI: 10.1107/S2059798316012225 Download PDF

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

J. Chem. Theory Comput., (2016) 12, 2611-2632
DOI: 10.1021/acs.jctc.6b00198 Download PDF

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

J. Chem. Phys., (2016) 144, 164115
DOI: 10.1063/1.4946779 Download PDF

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