Genomic Fold Assignment and Rational Modeling of Proteins of Biological Interest. - J. Michael Sauder; Roland L. Dunbrack Jr. (ISMB, 2000)

BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. - Jeffrey D. Grant; Roland L. Dunbrack Jr.; Frank J. Manion; Michael F. Ochs (Bioinform., 2002)

CASA: a server for the critical assessment of protein sequence alignment accuracy. - Robel Y. Kahsay; Guoli Wang 005; Nataraj Dongre; Guang R. Gao; Roland L. Dunbrack Jr. (Bioinform., 2002)

PISCES: a protein sequence culling server. - Guoli Wang 005; Roland L. Dunbrack Jr. (Bioinform., 2003)

MollDE: a homology modeling framework you can click with. - Adrian A. Canutescu; Roland L. Dunbrack Jr. (Bioinform., 2005)

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. - Robel Y. Kahsay; Guoli Wang 005; Guang R. Gao; Li Liao; Roland L. Dunbrack Jr. (Bioinform., 2005)

PISCES: recent improvements to a PDB sequence culling server. - Guoli Wang 005; Roland L. Dunbrack Jr. (Nucleic Acids Res., 2005)

ProtBuD: a database of biological unit structures of protein families and superfamilies. - Qifang Xu; Adrian A. Canutescu; Zoran Obradovic; Roland L. Dunbrack Jr. (Bioinform., 2006)

BioDownloader: bioinformatics downloads and updates in a few clicks. - Maxim V. Shapovalov; Adrian A. Canutescu; Roland L. Dunbrack Jr. (Bioinform., 2007)

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)

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model. - Daniel Ting; Guoli Wang 005; Maxim V. Shapovalov; Rajib Mitra; Michael I. Jordan; Roland L. Dunbrack Jr. (PLoS Comput. Biol., 2010)

The protein common interface database (ProtCID) - a comprehensive database of interactions of homologous proteins in multiple crystal forms. - Qifang Xu; Roland L. Dunbrack Jr. (Nucleic Acids Res., 2011)

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. - Qifang Xu; Roland L. Dunbrack Jr. (Bioinform., 2012)

Charge asymmetry in the proteins of the outer membrane. - Joanna S. G. Slusky; Roland L. Dunbrack Jr. (Bioinform., 2013)

PyIgClassify: a database of antibody CDR structural classifications. - Jared Adolf-Bryfogle; Qifang Xu; Benjamin North; Andreas Lehmann; Roland L. Dunbrack Jr. (Nucleic Acids Res., 2015)

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. - Jared Adolf-Bryfogle; Oleksandr Kalyuzhniy; Michael Kubitz; Brian D. Weitzner; Xiaozhen Hu; Yumiko Adachi; William R. Schief; Roland L. Dunbrack Jr. (PLoS Comput. Biol., 2018)

A new clustering and nomenclature for beta turns derived from high-resolution protein structures. - Maxim V. Shapovalov; Slobodan Vucetic; Roland L. Dunbrack Jr. (PLoS Comput. Biol., 2019)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Kincore: a web resource for structural classification of protein kinases and their inhibitors. - Vivek Modi; Roland L. Dunbrack Jr. (Nucleic Acids Res., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

The protein common assembly database (ProtCAD) - a comprehensive structural resource of protein complexes. - Qifang Xu; Roland L. Dunbrack Jr. (Nucleic Acids Res., 2023)