Accelerating molecular modeling applications with graphics processors. - John E. Stone; James C. Phillips; Peter L. Freddolino; David J. Hardy; Leonardo G. Trabuco; Klaus Schulten (J. Comput. Chem., 2007)

Stereochemical errors and their implications to molecular dynamics simulations. - Eduard Schreiner; Leonardo G. Trabuco; Peter L. Freddolino; Klaus Schulten (BMC Bioinform., 2011)

COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. - Chengxin Zhang; Peter L. Freddolino; Yang Zhang 040 (Nucleic Acids Res., 2017)

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. - Xiaoqiong Wei; Chengxin Zhang; Peter L. Freddolino; Yang Zhang 040; Zhiyong Lu (Bioinform., 2020)

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. - Wei Zheng 013; Qiqige Wuyun; Xiaogen Zhou; Yang Li 107; Peter L. Freddolino; Yang Zhang 040 (Nucleic Acids Res., 2022)

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. - Yi-Heng Zhu 001; Chengxin Zhang; Yan Liu 038; Gilbert S. Omenn; Peter L. Freddolino; Dong-Jun Yu; Yang Zhang 040 (Genom. Proteom. Bioinform., 2022)

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. - Mariano Spivak; John E. Stone; João Ribeiro 003; Jan Saam; Peter L. Freddolino; Rafael C. Bernardi; Emad Tajkhorshid (J. Chem. Inf. Model., 2023)

DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. - Ziying Zhang; Yaxian Cai; Biao Zhang; Wei Zheng 013; Peter L. Freddolino; Guijun Zhang; Xiaogen Zhou (Briefings Bioinform., 2024)