A Hierarchical Approach for Parallelization of a Global Optimization Method for Protein Structure Prediction. - Silvia N. Crivelli; Teresa Head-Gordon; Richard H. Byrd; Elizabeth Eskow; Robert B. Schnabel (Euro-Par, 1999)

Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding. - Jon M. Sorenson; Teresa Head-Gordon (RECOMB, 2000)

A Global Optimization Strategy for Predicting -helical Protein Tertiary Structure. - Silvia N. Crivelli; Richard H. Byrd; Elizabeth Eskow; Robert B. Schnabel; Richard Yu; Thomas M. Philip; Teresa Head-Gordon (Comput. Chem., 2000)

Matching Simulation and Experiment: A New Simplified Model for Simulating Protein Folding. - Jon M. Sorenson; Teresa Head-Gordon (J. Comput. Biol., 2000)

Computational challenges in structural and functional genomics. - Teresa Head-Gordon; John C. Wooley (IBM Syst. J., 2001)

Protein Engineering Study of Protein L by Simulation. - Jon M. Sorenson; Teresa Head-Gordon (J. Comput. Biol., 2002)

Cool walking: A new Markov chain Monte Carlo sampling method. - Scott Brown; Teresa Head-Gordon (J. Comput. Chem., 2003)

A new load-balancing strategy for the solution of dynamical large-tree-search problems using a hierarchical approach. - Silvia N. Crivelli; Teresa Head-Gordon (IBM J. Res. Dev., 2004)

An optimization approach to the problem of protein structure prediction. - Elizabeth Eskow; Brett W. Bader; Richard H. Byrd; Silvia N. Crivelli; Teresa Head-Gordon; Vincent Lamberti; Robert B. Schnabel (Math. Program., 2004)

How hot? Systematic convergence of the replica exchange method using multiple reservoirs. - Jory Z. Ruscio; Nicolas L. Fawzi; Teresa Head-Gordon (J. Comput. Chem., 2010)

Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles. - Jonathan E. Kohn; Pavel V. Afonine; Jory Z. Ruscio; Paul D. Adams; Teresa Head-Gordon (PLoS Comput. Biol., 2010)

Reliable protein structure refinement using a physical energy function. - Matthew S. Lin; Teresa Head-Gordon (J. Comput. Chem., 2011)

The Dynamical Mechanism of Auto-Inhibition of AMP-Activated Protein Kinase. - Cheng Peng; Teresa Head-Gordon (PLoS Comput. Biol., 2011)

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. - Lisa E. Felberg; David H. Brookes; Eng-Hui Yap; Elizabeth Jurrus; Nathan A. Baker; Teresa Head-Gordon (J. Comput. Chem., 2017)

Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction. - Xingyi Guan; Itai Leven; Farnaz Heidar-Zadeh; Teresa Head-Gordon (J. Chem. Inf. Model., 2021)

Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation. - Dong An; Sara Y. Cheng; Teresa Head-Gordon; Lin Lin 001; Jianfeng Lu 001 (J. Comput. Phys., 2021)

Using machine learning to go beyond potential energy surface benchmarking for chemical reactivity. - Xingyi Guan; Joseph P. Heindel; Taehee Ko; Chao Yang; Teresa Head-Gordon (Nat. Comput. Sci., 2023)

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Zi Hao Liu; Oufan Zhang; João M. C. Teixeira; Jie Li 072; Teresa Head-Gordon; Julie D. Forman-Kay (Zenodo, 2023)

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Zi Hao Liu; Oufan Zhang; João M. C. Teixeira; Jie Li 072; Teresa Head-Gordon; Julie D. Forman-Kay (J. Open Source Softw., 2023)

Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments. - Zi Hao Liu; João M. C. Teixeira; Oufan Zhang; Thomas E. Tsangaris; Jie Li 072; Claudiu C. Gradinaru; Teresa Head-Gordon; Julie D. Forman-Kay (Bioinform., 2023)

SmileyLlama: Modifying Large Language Models for Directed Chemical Space Exploration. - Joseph M. Cavanagh; Kunyang Sun; Andrew Gritsevskiy; Dorian Bagni; Thomas D. Bannister; Teresa Head-Gordon (CoRR, 2024)

Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. - Jie Li 072; Oufan Zhang; Kunyang Sun; Yingze Wang; Xingyi Guan; Dorian Bagni; Mojtaba Haghighatlari; Fiona L. Kearns; Conor D. Parks; Rommie E. Amaro; Teresa Head-Gordon (J. Chem. Inf. Model., 2024)

SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models. - Kunyang Sun; Dorian Bagni; Joseph M. Cavanagh; Yingze Wang; Jacob M. Sawyer; Andrew Gritsevskiy; Teresa Head-Gordon (CoRR, 2025)