Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. - Djamal Bouzida; Sandra Arthurs; Anthony B. Colson; Stephan T. Freer; Daniel K. Gehlhaar; Veda Larson; Brock A. Luty; Paul A. Rejto; Peter W. Rose; Gennady Verkhivker (Pacific Symposium on Biocomputing, 1999)

Deciphering common failures in molecular docking of ligand-protein complexes. - Gennady Verkhivker; Djamal Bouzida; Daniel K. Gehlhaar; Paul A. Rejto; Sandra Arthurs; Anthony B. Colson; Stephan T. Freer; Veda Larson; Brock A. Luty; Tami Marrone; Peter W. Rose (J. Comput. Aided Mol. Des., 2000)

Pre-calculated protein structure alignments at the RCSB PDB website. - Andreas Prlic; Spencer Bliven; Peter W. Rose; Wolfgang Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (Bioinform., 2010)

Integration of open access literature into the RCSB Protein Data Bank using BioLit. - Andreas Prlic; Marco A. Martinez; Dimitris Dimitropoulos; Bojan Beran; Benjamin T. Yukich; Peter W. Rose; Philip E. Bourne; J. Lynn Fink (BMC Bioinform., 2010)

Will Widgets and Semantic Tagging Change Computational Biology? - Philip E. Bourne; Bojan Beran; Chunxiao Bi; Wolfgang Bluhm; Roland L. Dunbrack Jr.; Andreas Prlic; Greg B. Quinn; Peter W. Rose; Raship Shah; Wendy Tao; Brian D. Weitzner; Benjamin T. Yukich (PLoS Comput. Biol., 2010)

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. - Wolfgang Bluhm; Bojan Beran; Chunxiao Bi; Dimitris Dimitropoulos; Andreas Prlic; Greg B. Quinn; Peter W. Rose; Chaitali Shah; Jasmine Young; Benjamin T. Yukich; Helen M. Berman; Philip E. Bourne (Database J. Biol. Databases Curation, 2011)

The RCSB Protein Data Bank: redesigned web site and web services. - Peter W. Rose; Bojan Beran; Chunxiao Bi; Wolfgang Bluhm; Dimitris Dimitropoulos; David S. Goodsell; Andreas Prlic; Martha Quesada; Greg B. Quinn; John D. Westbrook; Jasmine Young; Benjamin T. Yukich; et al. (Nucleic Acids Res., 2011)

BioJava: an open-source framework for bioinformatics in 2012. - Andreas Prlic; Andrew D. Yates; Spencer Bliven; Peter W. Rose; Julius O. B. Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard C. G. Holland; Gediminas Rimsa; et al. (Bioinform., 2012)

The RCSB Protein Data Bank: new resources for research and education. - Peter W. Rose; Chunxiao Bi; Wolfgang Bluhm; Cole H. Christie; Dimitris Dimitropoulos; Shuchismita Dutta; Rachel Kramer Green; David S. Goodsell; Andreas Prlic; Martha Quesada; Greg B. Quinn; Alexander G. Ramos; et al. (Nucleic Acids Res., 2013)

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. - Gregory B. Quinn; Chunxiao Bi; Cole H. Christie; Kyle Pang; Andreas Prlic; Takanori Nakane; Christine Zardecki; Maria Voigt; Helen M. Berman; Philip E. Bourne; Peter W. Rose (Bioinform., 2015)

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. - Peter W. Rose; Andreas Prlic; Chunxiao Bi; Wolfgang Bluhm; Cole H. Christie; Shuchismita Dutta; Rachel Kramer Green; David S. Goodsell; John D. Westbrook; Jesse Woo; Jasmine Young; Christine Zardecki; et al. (Nucleic Acids Res., 2015)

Web-based molecular graphics for large complexes. - Alexander S. Rose; Anthony R. Bradley; Yana Valasatava; Jose M. Duarte; Andreas Prlic; Peter W. Rose (Web3D, 2016)

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. - Andreas Prlic; Tara Kalro; Roshni Bhattacharya; Cole H. Christie; Stephen K. Burley; Peter W. Rose (Bioinform., 2016)

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. - Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang Bluhm; Dimitris Dimitropoulos; Dong Xu 002; Philip E. Bourne; Peter W. Rose (Bioinform., 2017)

The need for scientific software engineering in the pharmaceutical industry. - Brock A. Luty; Peter W. Rose (J. Comput. Aided Mol. Des., 2017)

The RCSB protein data bank: integrative view of protein, gene and 3D structural information. - Peter W. Rose; Andreas Prlic; Ali Altunkaya; Chunxiao Bi; Anthony R. Bradley; Cole H. Christie; Luigi Di Costanzo; Jose M. Duarte; Shuchismita Dutta; Zukang Feng; Rachel Kramer Green; David S. Goodsell; et al. (Nucleic Acids Res., 2017)

MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures. - Anthony R. Bradley; Alexander S. Rose; Antonín Pavelka; Yana Valasatava; Jose M. Duarte; Andreas Prlic; Peter W. Rose (PLoS Comput. Biol., 2017)

NGL viewer: web-based molecular graphics for large complexes. - Alexander S. Rose; Anthony R. Bradley; Yana Valasatava; Jose M. Duarte; Andreas Prlic; Peter W. Rose (Bioinform., 2018)

Ten Simple Rules for Reproducible Research in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (CoRR, 2018)

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. - Stephen K. Burley; Helen M. Berman; Charmi Bhikadiya; Chunxiao Bi; Li Chen 022; Luigi Di Costanzo; Cole H. Christie; Kenneth Dalenberg; Jose M. Duarte; Shuchismita Dutta; Zukang Feng; Sutapa Ghosh; et al. (Nucleic Acids Res., 2019)

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. - Spencer E. Bliven; Aleix Lafita; Peter W. Rose; Guido Capitani; Andreas Prlic; Philip E. Bourne (PLoS Comput. Biol., 2019)

BioJava 5: A community driven open-source bioinformatics library. - Aleix Lafita; Spencer Bliven; Andreas Prlic; Dmytro Guzenko; Peter W. Rose; Anthony R. Bradley; Paolo Pavan; Douglas Myers-Turnbull; Yana Valasatava; Michael L. Heuer; Matt Larson; Stephen K. Burley; et al. (PLoS Comput. Biol., 2019)

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (PLoS Comput. Biol., 2019)

Ten simple rules to cultivate transdisciplinary collaboration in data science. - Faryad Sahneh; Meghan A. Balk; Marina Kisley; Chi-Kwan Chan; Mercury Fox; Brian Nord; Eric Lyons 002; Tyson Lee Swetnam; Daniela Huppenkothen; Will Sutherland; Ramona L. Walls; Daven P. Quinn; et al. (PLoS Comput. Biol., 2021)

IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements. - Shiqiang Tao; Wei-Chun Chou; Jianfu Li; Jingcheng Du; Pritham Ram; Rashmie Abeysinghe; Hua Xu 001; Xiaoqian Jiang; Peter W. Rose; Lucila Ohno-Machado; Guo-Qiang Zhang 001 (ICHI, 2022)

A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology. - Sergio E. Baranzini; Katy Börner; John H. Morris; Charlotte A. Nelson; Karthik Soman; Erica Schleimer; Michael J. Keiser; Mark A. Musen; Roger Pearce; Tahsin Reza; Brett Smith; Bruce William Herr II; et al. (AI Mag., 2022)

The Pfizer Crystal Structure Database: An essential tool for structure-based design at Pfizer. - Daniel K. Gehlhaar; Brock A. Luty; Philip P. Cheung; Andy H. Litman; Robert M. Owen; Peter W. Rose (J. Comput. Chem., 2022)

Developing a Best Practices Training Program in Cyberinfrastructure-Enabled Machine Learning Research. - Mary P. Thomas; Andreas W. Götz; Martin C. Kandes; Mai H. Nguyen; Paul Rodríguez; Peter W. Rose; Robert S. Sinkovits (PEARC, 2023)

Biomedical knowledge graph-enhanced prompt generation for large language models. - Karthik Soman; Peter W. Rose; John H. Morris; Rabia E. Akbas; Brett Smith; Braian Peetoom; Catalina Villouta-Reyes; Gabriel Cerono; Yongmei Shi; Angela Rizk-Jackson; Sharat Israni; Charlotte A. Nelson; et al. (CoRR, 2023)

The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. - John H. Morris; Karthik Soman; Rabia E. Akbas; Xiaoyuan Zhou; Brett Smith; Elaine C. Meng; Conrad C. Huang; Gabriel Cerono; Gundolf Schenk; Angela Rizk-Jackson; Adil Harroud; Lauren M. Sanders; et al. (Bioinform., 2023)