Nagarajan Vaidehi

发表

Atomic-level simulation and modeling of biomacromolecules

William A. Goddard, Nagarajan Vaidehi, W. Goddard, 2001 .

Molecular dynamics for very large systems on massively parallel computers: The MPSim program

Sharon Brunett, Kian-Tat Lim, William A. Goddard, 1997 .

Advanced techniques for constrained internal coordinate molecular dynamics

Abhinandan Jain, Jeffrey R. Wagner, Nagarajan Vaidehi, 2013, J. Comput. Chem..

The MPSim‐Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals

William A. Goddard, Art E. Cho, Peter M. Kekenes-Huskey, 2005, J. Comput. Chem..

Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

Abhinandan Jain, Nagarajan Vaidehi, Abhinandan Jain, 2014, The journal of physical chemistry. B.

GPCRTooKit: A Computational Platform for Structural Comparison of GPCR Crystal Structures and Homology Model Refinement

Nagarajan Vaidehi, Supriyo Bhattacharya, Adrien B. Larsen, 2012 .

GNEIMO: Constrained Molecular Dynamics Methods For Long Time Scale Simulation of Macromolecules

Abhinandan Jain, Rudranarayan Mukherjee, Nagarajan Vaidehi, 2010 .

Importance of Receptor Flexibility in Binding of Cyclam Compounds to the Chemokine Receptor CXCR4

Kevin Patel, Spencer Hall, Nagarajan Vaidehi, 2011, J. Chem. Inf. Model..

Molecular dynamics for very large systems on massively parallel computers: The MPSim program

Stephen Taylor, Sharon Brunett, Kian-Tat Lim, 1997, J. Comput. Chem..

GNEIMO Constrained Dynamics Method: A Tool for Protein Structure Refinement and Conformational Changes

Nagarajan Vaidehi, 2012 .

Prediction of Conformation Specific Thermostabilizing Mutations for Class A GPCRs.

Nagarajan Vaidehi, Benjamin Levy, Suvamay Jana, 2019, Journal of chemical information and modeling.

Computational Method To Identify Druggable Binding Sites That Target Protein-Protein Interactions

Hubert Li, Christofer S. Tautermann, Daniel Seeliger, 2014, J. Chem. Inf. Model..

A fast recursive algorithm for molecular dynamics simulation

Abhinandan Jain, Nagarajan Vaidehi, Guillermo Rodriguez, 1993 .

GneimoSim: A modular internal coordinates molecular dynamics simulation package

Jeffrey R. Wagner, Abhinandan Jain, Romelia Salomón-Ferrer, 2014, J. Comput. Chem..

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1

Jianping Lin, Abdelazize Laoui, Spencer Hall, 2010, J. Comput. Aided Mol. Des..

Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method

Abhinandan Jain, Jeffrey R. Wagner, Nagarajan Vaidehi, 2014, J. Chem. Inf. Model..

Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors.

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2008, Journal of molecular biology.

Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

William A. Goddard, Tahir Cagin, Siddharth Dasgupta, 2001 .

Modeling the human PTC bitter-taste receptor interactions with bitter tastants

Nagarajan Vaidehi, Wely B. Floriano, Dennis Drayna, 2006, Journal of molecular modeling.

Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase.

Nagarajan Vaidehi, William A Goddard, David A Tirrell, 2002, Journal of the American Chemical Society.

Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation.

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2008, Biophysical journal.

The role of conformational ensembles in ligand recognition in G-protein coupled receptors.

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2011, Journal of the American Chemical Society.

Fidelity of Phenylalanyl-tRNA Synthetase in Binding the Natural Amino Acids

William A. Goddard, Peter M. Kekenes-Huskey, Nagarajan Vaidehi, 2003 .

LITiCon: a discrete conformational sampling computational method for mapping various functionally selective conformational states of transmembrane helical proteins.

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2012, Methods in molecular biology.

The Predicted 3D Structures of the Human M1 Muscarinic Acetylcholine Receptor with Agonist or Antagonist Bound

Nagarajan Vaidehi, William A Goddard, W. Goddard, 2006, ChemMedChem.

Identification of Anti-Malarial Compounds as Novel Antagonists to Chemokine Receptor CXCR4 in Pancreatic Cancer Cells

Nagarajan Vaidehi, Jianming Lu, N. Vaidehi, 2012, PloS one.

Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.

Abhinandan Jain, Nagarajan Vaidehi, In-Hee Park, 2012, The journal of physical chemistry. B.

Predicted 3 D structure for the human 2 adrenergic receptor and its binding site for agonists and antagonists

William A. Goddard, Peter L. Freddolino, Nagarajan Vaidehi, 2004 .

Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors.

Nagarajan Vaidehi, Wely B. Floriano, William A Goddard, 2004, Chemical senses.

Equipartition Principle for Internal Coordinate Molecular Dynamics.

Abhinandan Jain, Nagarajan Vaidehi, In-Hee Park, 2012, Journal of chemical theory and computation.

The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number.

Prabal K Maiti, Nagarajan Vaidehi, William A Goddard, 2004, Nucleic acids research.

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Peter Spijker, Nagarajan Vaidehi, Albert J. Markvoort, 2010, International journal of molecular sciences.

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

Nagarajan Vaidehi, William A Goddard, W. Goddard, 2004, Biophysical journal.

Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site.

Jiyoung Heo, Nagarajan Vaidehi, William A Goddard, 2007, Journal of molecular graphics & modelling.

Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution.

Jiyoung Heo, Prabal K Maiti, Nagarajan Vaidehi, 2006, Biophysical journal.

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

Peter L. Freddolino, Nagarajan Vaidehi, William A Goddard, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of structure and function of G protein-coupled receptors

Peter L. Freddolino, Nagarajan Vaidehi, Wely B. Floriano, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Sulfation patterns of glycosaminoglycans encode molecular recognition and activity

Nagarajan Vaidehi, Linda C Hsieh-Wilson, A. Nishi, 2006, Nature chemical biology.

Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists.

Nagarajan Vaidehi, N. Vaidehi, B. M. Forman, 2015, Bioorganic & medicinal chemistry.

Modeling small molecule-compound binding to G-protein-coupled receptors.

Nagarajan Vaidehi, N. Vaidehi, R. Horuk, 2009, Methods in enzymology.

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists.

Peter L. Freddolino, Nagarajan Vaidehi, Wely B. Floriano, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Test of the Binding Threshold Hypothesis for olfactory receptors: Explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912‐93

Nagarajan Vaidehi, Wely B. Floriano, William A Goddard, 2005, Protein science : a publication of the Protein Society.

Predictions of CCR1 Chemokine Receptor Structure and BX 471 Antagonist Binding Followed by Experimental Validation*

Ravinder Abrol, Nagarajan Vaidehi, Wely B. Floriano, 2006, Journal of Biological Chemistry.

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction.

Nagarajan Vaidehi, Kyle E. Roberts, N. Vaidehi, 2009, Journal of molecular graphics & modelling.

Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors

Christopher G. Tate, Nagarajan Vaidehi, Supriyo Bhattacharya, 2014, Journal of chemical theory and computation.

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

Nagarajan Vaidehi, Wely B. Floriano, William A Goddard, 2004, Journal of medicinal chemistry.

Critical analysis of the successes and failures of homology models of G protein‐coupled receptors

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2013, Proteins.

Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor.

Nagarajan Vaidehi, Supriyo Bhattacharya, N. Vaidehi, 2010, Journal of the American Chemical Society.

Dynamics and flexibility of G-protein-coupled receptor conformations and their relevance to drug design.

Nagarajan Vaidehi, N. Vaidehi, 2010, Drug discovery today.

Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist.

Peter L. Freddolino, Peter Spijker, Nagarajan Vaidehi, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist.

Abdelazize Laoui, Stephan Reiling, Lan Mu, 2007, Journal of the American Chemical Society.

Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment.

Nagarajan Vaidehi, Wely B. Floriano, William A Goddard, 2004, Chemical senses.