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New Publications

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

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

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

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

ACS Catal., (2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158 Download PDF

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

DOI: 10.1021/bk-2016-1217.ch009

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

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

A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

DOI: 10.4032/9789814613934 Download PDF

Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation

J. Am. Chem. Soc., (2016) 138, 3058-3065
DOI: 10.1021/jacs.5b12061 Download PDF

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