A distance geometry heuristic for expanding the range of geometries sampled during conformational search. - Sergei Izrailev; Fangqiang Zhu; Dimitris K. Agrafiotis (J. Comput. Chem., 2006)

Self-organizing superimposition algorithm for conformational sampling. - Fangqiang Zhu; Dimitris K. Agrafiotis (J. Comput. Chem., 2007)

Conformational Sampling of Bioactive Molecules: A Comparative Study. - Dimitris K. Agrafiotis; Alan C. Gibbs; Fangqiang Zhu; Sergei Izrailev; Eric J. Martin (J. Chem. Inf. Model., 2007)

Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification. - Fangqiang Zhu; Dimitris K. Agrafiotis (J. Chem. Inf. Model., 2007)

Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss. - Pascal Bonnet; Dimitris K. Agrafiotis; Fangqiang Zhu; Eric J. Martin (J. Chem. Inf. Model., 2009)

A Self-Organizing Algorithm for Modeling Protein Loops. - Pu Liu; Fangqiang Zhu; Dmitrii N. Rassokhin; Dimitris K. Agrafiotis (PLoS Comput. Biol., 2009)

Convergence and error estimation in free energy calculations using the weighted histogram analysis method. - Fangqiang Zhu; Gerhard Hummer (J. Comput. Chem., 2012)

Monte Carlo Simulations of HIV Capsid Protein Homodimer. - Fangqiang Zhu; Bo Chen (J. Chem. Inf. Model., 2015)

Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein. - Hao Sha; Fangqiang Zhu (J. Chem. Inf. Model., 2017)

Calculating Single-Channel Permeability and Conductance from Transition Paths. - Xiaoyan Zhou; Fangqiang Zhu (J. Chem. Inf. Model., 2019)

Binding Affinity Prediction by Pairwise Function Based on Neural Network. - Fangqiang Zhu; Xiaohua Zhang; Jonathan E. Allen; Derek Jones; Felice C. Lightstone (J. Chem. Inf. Model., 2020)

High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models. - Garrett A. Stevenson; Derek Jones; Hyojin Kim 001; W. F. Drew Bennett; Brian J. Bennion; Monica Borucki; Feliza Bourguet; Aidan Epstein; Magdalena Franco; Brooke Harmon; Stewart He; Max P. Katz; et al. (SC, 2021)