First-Author Publications
11
In Prep
PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants
In Prep
cryoWEight: An automated framework for iterative ensemble cryo-EM-guided reweighting for biomolecular complexes
bioRxiv
seekrflow: Towards an end-to-end automated simulation pipeline with machine-learned force field for accelerated drug-target kinetic and thermodynamic predictions
IUCr
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation
ACS
Advances and challenges in milestoning simulations for drug-target kinetics
LiveCoMS
An introductory tutorial to the SEEKR2 multiscale milestoning software [Article v1.0]
RSC
QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
ACS
Selectivity and rank ordering of tight-binding JAK-STAT pathway inhibitors using Markovian milestoning with Voronoi tessellation simulations
ACS
DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling
ACS
Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling
MDPI
Molecular Properties of Drugs Handled by Kidney OATs and Liver OATPs Revealed by Chemoinformatics and Machine Learning
Co-Author Publications
11
In Prep
Deep learning algorithms identify CD27 mutations with improved predicted CD70 binding
arXiv
The Denario project: Deep knowledge AI agents for scientific discovery
Elsevier
MXenes at the Interface of Biology and Materials for Biomedical Applications
ACS
Prediction of Threonine-Tyrosine Kinase Receptor–Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics
Nature
Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens
MDPI
Distinguishing Molecular Properties of OAT, OATP, and MRP Drug Substrates by Machine Learning
ACS
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine
ACS
Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach
Elsevier
Paper based field deployable sensor for naked eye monitoring of copper (II) ions; elucidation of binding mechanism by DFT studies
ACS
Water-Stable Nanoscale Zirconium-Based Metal-Organic Frameworks for the Effective Removal of Glyphosate from Aqueous Media
ACS
Turn-on Fluorescence Sensing and Discriminative Detection of Aliphatic Amines Using a 5-Fold-Interpenetrated Coordination Polymer