Molecular dynamics for very large systems on massively parallel computers: The MPSim program. - Kian-Tat Lim; Sharon Brunett; Mihail Iotov; Richard B. McClurg; Nagarajan Vaidehi; Siddharth Dasgupta; Stephen Taylor; William A. Goddard III (J. Comput. Chem., 1997)

The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals. - Art E. Cho; John A. Wendel; Nagarajan Vaidehi; Peter M. Kekenes-Huskey; Wely B. Floriano; Prabal K. Maiti; William A. Goddard III (J. Comput. Chem., 2005)

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1. - Supriyo Bhattacharya; Govindan Subramanian; Spencer Hall; Jianping Lin; Abdelazize Laoui; Nagarajan Vaidehi (J. Comput. Aided Mol. Des., 2010)

Importance of Receptor Flexibility in Binding of Cyclam Compounds to the Chemokine Receptor CXCR4. - Alfonso Lam; Supriyo Bhattacharya; Kevin Patel; Spencer Hall; Allen Mao; Nagarajan Vaidehi (J. Chem. Inf. Model., 2011)

Advanced techniques for constrained internal coordinate molecular dynamics. - Jeffrey R. Wagner; Gouthaman S. Balaraman; Michiel J. M. Niesen; Adrien B. Larsen; Abhinandan Jain; Nagarajan Vaidehi (J. Comput. Chem., 2013)

GneimoSim: A modular internal coordinates molecular dynamics simulation package. - Adrien B. Larsen; Jeffrey R. Wagner; Saugat Kandel; Romelia Salomón-Ferrer; Nagarajan Vaidehi; Abhinandan Jain (J. Comput. Chem., 2014)

Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method. - Adrien B. Larsen; Jeffrey R. Wagner; Abhinandan Jain; Nagarajan Vaidehi (J. Chem. Inf. Model., 2014)

Computational Method To Identify Druggable Binding Sites That Target Protein-Protein Interactions. - Hubert Li; Vinod Kasam; Christofer S. Tautermann; Daniel Seeliger; Nagarajan Vaidehi (J. Chem. Inf. Model., 2014)

How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins? - Hubert Li; Manbir Sandhu; Linda H. Malkas; Robert J. Hickey; Nagarajan Vaidehi (J. Chem. Inf. Model., 2017)

Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. - Suvamay Jana; Soumadwip Ghosh; Sanychen Muk; Benjamin Levy; Nagarajan Vaidehi (J. Chem. Inf. Model., 2019)

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories. - Elizaveta Mukhaleva; Babgen Manookian; Hanyu Chen; Indira R. Sivaraj; Ning Ma; Wenyuan Wei; Konstancja Urbaniak; Grigoriy Gogoshin; Supriyo Bhattacharya; Nagarajan Vaidehi; Andrei S. Rodin; Sergio Branciamore (J. Chem. Inf. Model., 2025)