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Roland Dunbrack, Ph.D. - Publications

Affiliations: 
Computer and Information Science Temple University, Philadelphia, PA, United States 
Area:
Information Science, Computer Science, Bioinformatics Biology
Website:
http://dunbrack.fccc.edu
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58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032]. Heliyon. 9: e17901. PMID 37701412 DOI: 10.1016/j.heliyon.2023.e17901  0.671
2023 Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LA, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin AMJJ, Savojardo C, ... ... Dunbrack RL, et al. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics. e2200323. PMID 37365936 DOI: 10.1002/pmic.202200323  0.458
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus. Heliyon. 9: e15032. PMID 37035348 DOI: 10.1016/j.heliyon.2023.e15032  0.684
2023 Wasserman JS, Faezov B, Patel KR, Kurimchak AN, Palacio SM, Fowle H, McEwan BC, Xu Q, Zhao Z, Cressey L, Johnson N, Duncan JS, Kettenbach AN, Dunbrack RL, Graña X. FAM122A ensures cell cycle interphase progression and checkpoint control as a SLiM-dependent substrate-competitive inhibitor to the B55⍺/PP2A phosphatase. Biorxiv : the Preprint Server For Biology. PMID 36945596 DOI: 10.1101/2023.03.06.531310  0.413
2022 Xu Q, Dunbrack RL. The protein common assembly database (ProtCAD)-a comprehensive structural resource of protein complexes. Nucleic Acids Research. PMID 36300618 DOI: 10.1093/nar/gkac937  0.458
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, ... ... Dunbrack RL, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147  0.76
2021 Fowle H, Zhao Z, Xu Q, Wasserman JS, Wang X, Adeyemi M, Feiser F, Kurimchak AN, Atar D, McEwan BC, Kettenbach AN, Page R, Peti W, Dunbrack RL, Graña X. PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107. Elife. 10. PMID 34661528 DOI: 10.7554/eLife.63181  0.42
2020 Kelow SP, Adolf-Bryfogle J, Dunbrack RL. Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding. Mabs. 12: 1840005. PMID 33180672 DOI: 10.1080/19420862.2020.1840005  0.681
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Dunbrack R, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.751
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Dunbrack R, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.749
2020 Xu Q, Dunbrack RL. ProtCID: a data resource for structural information on protein interactions. Nature Communications. 11: 711. PMID 32024829 DOI: 10.1038/S41467-020-14301-4  0.457
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.736
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.746
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.735
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.725
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.733
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003  0.75
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.737
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Dunbrack R, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.726
2019 Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, et al. Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Human Mutation. PMID 31342580 DOI: 10.1002/Humu.23875  0.608
2019 Kueppers F, Andrake MD, Xu Q, Dunbrack RL, Kim J, Sanders CL. Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency. Bmc Medical Genetics. 20: 125. PMID 31307431 DOI: 10.1186/S12881-019-0852-5  0.381
2019 Xu Q, Dunbrack RL. Principles and characteristics of biological assemblies in experimentally determined protein structures. Current Opinion in Structural Biology. 55: 34-49. PMID 30965224 DOI: 10.1016/J.Sbi.2019.03.006  0.447
2018 Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. Plos Computational Biology. 14: e1006112. PMID 29702641 DOI: 10.1371/Journal.Pcbi.1006112  0.761
2017 Deihimi S, Lev A, Slifker M, Shagisultanova E, Xu Q, Jung K, Vijayvergia N, Ross EA, Xiu J, Swensen J, Gatalica Z, Andrake M, Dunbrack RL, El-Deiry WS. BRCA2, EGFR, and NTRK mutations in mismatch repair-deficient colorectal cancers with MSH2 or MLH1 mutations. Oncotarget. PMID 28591715 DOI: 10.18632/Oncotarget.18098  0.362
2017 Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, et al. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation. PMID 28440912 DOI: 10.1002/Humu.23235  0.621
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.482
2017 Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Human Mutation. PMID 28370845 DOI: 10.1002/Humu.23222  0.43
2017 Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nature Protocols. 12: 401-416. PMID 28125104 DOI: 10.1038/Nprot.2016.180  0.762
2016 Huwe PJ, Xu Q, Shapovalov MV, Modi V, Andrake MD, Dunbrack RL. Biological function derived from predicted structures in CASP11. Proteins. PMID 27181425 DOI: 10.1002/Prot.24997  0.444
2016 Modi V, Xu Q, Adhikari S, Dunbrack RL. Assessment of template-based modeling of protein structure in CASP11. Proteins. PMID 27081927 DOI: 10.1002/Prot.25049  0.432
2016 Deihimi S, Lev A, Shagisultanova E, Xiu J, Slifker M, Xu Q, Dicker DT, Ross EA, Dunbrack R, El-Deiry WS. Abstract 2751: Frequent BRCA2 somatic mutations in colorectal cancer patients with microsatellite instability (MSI) Cancer Research. 76: 2751-2751. DOI: 10.1158/1538-7445.Am2016-2751  0.433
2015 Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Science Signaling. 8: rs13. PMID 26628682 DOI: 10.1126/Scisignal.Aaa6711  0.413
2015 Weitzner BD, Dunbrack RL, Gray JJ. The origin of CDR H3 structural diversity. Structure (London, England : 1993). 23: 302-11. PMID 25579815 DOI: 10.1016/J.Str.2014.11.010  0.762
2015 Vijayan RS, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. Journal of Medicinal Chemistry. 58: 466-79. PMID 25478866 DOI: 10.1021/Jm501603H  0.409
2015 Adolf-Bryfogle J, Xu Q, North B, Lehmann A, Dunbrack RL. PyIgClassify: a database of antibody CDR structural classifications. Nucleic Acids Research. 43: D432-8. PMID 25392411 DOI: 10.1093/Nar/Gku1106  0.733
2015 Slusky J, Dunbrack R. Charge Asymmetry in Outer Membrane Proteins Biophysical Journal. 108: 240a-241a. DOI: 10.1016/J.Bpj.2014.11.1331  0.677
2014 Shapovalov MV, Wang Q, Xu Q, Andrake M, Dunbrack RL. BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers. Plos One. 9: e98309. PMID 24922057 DOI: 10.1371/Journal.Pone.0098309  0.445
2013 Adolf-Bryfogle J, Dunbrack RL. The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite. Plos One. 8: e66856. PMID 23874400 DOI: 10.1371/Journal.Pone.0066856  0.686
2013 Slusky JS, Dunbrack RL. Charge asymmetry in the proteins of the outer membrane. Bioinformatics (Oxford, England). 29: 2122-8. PMID 23782617 DOI: 10.1093/bioinformatics/btt355  0.666
2013 Wei Q, Xu Q, Dunbrack RL. Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins. 81: 199-213. PMID 22965855 DOI: 10.1002/Prot.24176  0.441
2012 Xu Q, Dunbrack RL. Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics (Oxford, England). 28: 2763-72. PMID 22942020 DOI: 10.1093/Bioinformatics/Bts533  0.418
2011 Xu Q, Dunbrack RL. The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Research. 39: D761-70. PMID 21036862 DOI: 10.1093/Nar/Gkq1059  0.451
2010 Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF. Development of a rotamer library for use in beta-peptide foldamer computational design. Journal of the American Chemical Society. 132: 7312-20. PMID 20446685 DOI: 10.1021/Ja906700X  0.415
2010 Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlić A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. Will widgets and semantic tagging change computational biology? Plos Computational Biology. 6: e1000673. PMID 20195550 DOI: 10.1371/Journal.Pcbi.1000673  0.715
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014  0.572
2009 Weitzner B, Meehan T, Xu Q, Dunbrack RL. An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Proteins. 75: 289-95. PMID 19173308 DOI: 10.1002/Prot.22347  0.741
2008 Xu Q, Canutescu AA, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL. Statistical analysis of interface similarity in crystals of homologous proteins. Journal of Molecular Biology. 381: 487-507. PMID 18599072 DOI: 10.1016/J.Jmb.2008.06.002  0.606
2006 Xu Q, Canutescu A, Obradovic Z, Dunbrack RL. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics (Oxford, England). 22: 2876-82. PMID 17018535 DOI: 10.1093/Bioinformatics/Btl490  0.625
2006 Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, et al. Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules Structure. 14: 1211-1217. PMID 16955948 DOI: 10.1016/J.Str.2006.06.005  0.401
2005 Kahsay RY, Wang G, Gao G, Liao L, Dunbrack R. Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics (Oxford, England). 21: 2287-93. PMID 15797916 DOI: 10.1093/Bioinformatics/Bti374  0.317
1997 Armand P, Kirshenbaum K, Falicov A, Dunbrack RL, Dill KA, Zuckermann RN, Cohen FE. Chiral N-substituted glycines can form stable helical conformations. Folding & Design. 2: 369-75. PMID 9427011 DOI: 10.1016/S1359-0278(97)00051-5  0.4
1997 Byington CL, Dunbrack RL, Whitby FG, Cohen FE, Agabian N. Entamoeba histolytica: computer-assisted modeling of phosphofructokinase for the prediction of broad-spectrum antiparasitic agents. Experimental Parasitology. 87: 194-202. PMID 9371084 DOI: 10.1006/Expr.1997.4224  0.385
1997 Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Science : a Publication of the Protein Society. 6: 1661-81. PMID 9260279 DOI: 10.1002/pro.5560060807  0.413
1997 Bower MJ, Cohen FE, Dunbrack RL. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. Journal of Molecular Biology. 267: 1268-82. PMID 9150411 DOI: 10.1006/jmbi.1997.0926  0.475
1997 Dunbrack RL, Gerloff DL, Bower M, Chen X, Lichtarge O, Cohen FE. Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. Folding & Design. 2: R27-42. PMID 9135979 DOI: 10.1016/S1359-0278(97)00011-4  0.451
1997 Byington CL, Dunbrack RL, Cohen FE, Agabian N. Molecular modeling of phosphofructokinase from Entamoeba histolytica for the prediction of new antiparasitic agents. Archives of Medical Research. 28: 86-8. PMID 9033023  0.386
1994 Dunbrack RL, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature Structural Biology. 1: 334-40. PMID 7664040 DOI: 10.1038/Nsb0594-334  0.373
1993 Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. Journal of Molecular Biology. 230: 543-74. PMID 8464064 DOI: 10.1006/Jmbi.1993.1170  0.379
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