A Bayesian Approach to Sequence Alignment Algorithms for Protein Structure Recognition. - Richard A. Goldstein; Zaida Luthey-Schulten; Peter G. Wolynes (HICSS (5), 1994)

Evaluating protein structure-prediction schemes using energy landscape theory. - Michael P. Eastwood; Corey Hardin; Zaida Luthey-Schulten; Peter G. Wolynes (IBM J. Res. Dev., 2001)

Folding funnels: The key to robust protein structure prediction. - Corey Hardin; Michael P. Eastwood; Michael C. Prentiss; Zaida Luthey-Schulten; Peter G. Wolynes (J. Comput. Chem., 2002)

Classical force field parameters for the heme prosthetic group of cytochrome c. - Felix Autenrieth; Emad Tajkhorshid; Jérôme Baudry; Zaida Luthey-Schulten (J. Comput. Chem., 2004)

Multiple Alignment of protein structures and sequences for VMD. - John Eargle; Dan Wright; Zaida Luthey-Schulten (Bioinform., 2006)

MultiSeq: unifying sequence and structure data for evolutionary analysis. - Elijah Roberts; John Eargle; Dan Wright; Zaida Luthey-Schulten (BMC Bioinform., 2006)

Visualizing the dual space of biological molecules. - John Eargle; Zaida Luthey-Schulten (Comput. Biol. Chem., 2006)

Long time-scale simulations of in vivo diffusion using GPU hardware. - Elijah Roberts; John E. Stone; Leonardo Sepulveda; Wen-mei W. Hwu; Zaida Luthey-Schulten (IPDPS, 2009)

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study. - Elijah Roberts; Andrew T. Magis; Julio O. Ortiz; Wolfgang Baumeister; Zaida Luthey-Schulten (PLoS Comput. Biol., 2011)

NetworkView: 3D display and analysis of protein·RNA interaction networks. - John Eargle; Zaida Luthey-Schulten (Bioinform., 2012)

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. - Elijah Roberts; John E. Stone; Zaida Luthey-Schulten (J. Comput. Chem., 2013)

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. - Michael J. Hallock; John E. Stone; Elijah Roberts; Corey Fry; Zaida Luthey-Schulten (Parallel Comput., 2014)

Spatially-resolved metabolic cooperativity within dense bacterial colonies. - John A. Cole; Lars Kohler; Jamila Hedhli; Zaida Luthey-Schulten (BMC Syst. Biol., 2015)

Improving Reaction Kernel Performance in Lattice Microbes: Particle-Wise Propensities and Run-Time Generated Code. - Michael J. Hallock; Zaida Luthey-Schulten (IPDPS Workshops, 2016)

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. - John E. Stone; Michael J. Hallock; James C. Phillips; Joseph R. Peterson; Zaida Luthey-Schulten; Klaus Schulten (IPDPS Workshops, 2016)

Population FBA predicts metabolic phenotypes in yeast. - Piyush Labhsetwar; Marcelo C. R. Melo; John A. Cole; Zaida Luthey-Schulten (PLoS Comput. Biol., 2017)

An in-silico human cell model reveals the influence of spatial organization on RNA splicing. - Zhaleh Ghaemi; Joseph R. Peterson; Martin Gruebele; Zaida Luthey-Schulten (PLoS Comput. Biol., 2020)

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. - Melih Sener; Stuart Levy; John E. Stone; A. J. Christensen 001; Barry Isralewitz; Robert Patterson; Kalina Borkiewicz; Jeffrey Carpenter; C. Neil Hunter; Zaida Luthey-Schulten; Donna J. Cox (Parallel Comput., 2021)