Faculty Summaries
Roland L Dunbrack, Jr, PhD
Roland L Dunbrack, Jr, PhD
  • Adjunct Associate Professor, University of Pennsylvania, School of Medicine
  • Adjunct Associate Professor, Drexel University College of Medicine
  • Director,
  • Director, Organic Synthesis Facility
Office Phone: 215-728-2434
Fax: 215-728-2412
Office: R465

2000 - present

  • North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol. 2011 Feb 18;406(2):228-56.
  • Xu QF, Dunbrack RL. The protein common interface database (ProtCID)-a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res. 2011 Jan;39:D761-D770.
  • Shapovalov MV, Dunbrack RL. A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions. Structure. 2011 Jun;19(6):844-58.
  • Bourne PE, Beran B, Bi CX, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. Will Widgets and Semantic Tagging Change Computational Biology?. Plos Computational Biology. 2010 Feb;6(2).
  • Tong X, Zitserman D, Serebriiskii I, Andrake M, Dunbrack R, Roegiers F. Numb Independently Antagonizes Sanpodo Membrane Targeting and Notch Signaling in Drosophila Sensory Organ Precursor Cells. Mol Biol Cell. 2010 Mar;21(5):802-10.
  • Egleston BL, Dunbrack RL, Hall MJ. Clinical Trials That Explicitly Exclude Gay and Lesbian Patients. N Engl J Med. 2010 Mar;362(11):1054-5.
  • Doulias PT, Greene JL, Greco TM, Tenopoulou M, Seeholzer SH, Dunbrack RL, Ischiropoulos H. Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A. 2010 Sep;107(39):16958-63.
  • Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: A meta-predictor of intrinsically disordered amino acids. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2010 Apr;1804(4):996-1010.
  • Hayik SA, Dunbrack R, Merz KM. Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein-Ligand Binding Affinity. Journal of Chemical Theory and Computation. 2010 Oct;6(10):3079-91.
  • Wei Q, Wang L, Wang Q, Kruger WD, Dunbrack RL. Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. Proteins. 2010 Jul;78(9):2058-74.
  • Plotnikova OV, Pugacheva EN, Dunbrack RL, Golemis EA. Rapid calcium-dependent activation of Aurora-A kinase. Nat Commun. 2010 Sep;1(6):1-8.
  • Shandler SJ, Shapovalov MV, Dunbrack RL, DeGrado WF. Development of a Rotamer Library for Use in beta-Peptide Foldamer Computational Design. J Am Chem Soc. 2010 Jun;132(21):7312-20.
  • Ting D, Wang GL, Shapovalov M, Mitra R, Jordan MI, Dunbrack RL. Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model. Plos Computational Biology. 2010 Apr;6(4).
  • Li C, Andrake M, Dunbrack R, Enders GH. A bi-functional regulatory element in human somatic Wee1 mediates cyclin A/Cdk2 binding and Crm1-dependent nuclear export. Molec Cell Biol. Forthcoming 2009. PubMed
  • Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA. Conformation dependence of backbone geometry in proteins. Structure. 2009;17:1316-25. PubMed
  • Krivov GG, Shapovalov MV, Dunbrack RL Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins. 2009;77:778-95. PubMed
  • Schwede T, Sali A, Honig B et al. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009;17(2):151-9. PubMed
  • Xu Q, Canutescu AA, Wang G et al. Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol. 2008;381(2):487-507. PubMed
  • Weitzner B, Meehan T, Xu Q et al. An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Proteins. 2008;75(2):289-95. PubMed
  • Wang Q, Dunbrack Jr RL. An Integrated Database for Complex Protein Structure Modeling. In: BIBM08. Series An Integrated Database for Complex Protein Structure Modeling. Philadelphia PA: IEEE; 2008.
  • Wang Q, Canutescu AA, Dunbrack RL, Jr. SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc. 2008;3(12):1832-47. PubMed
  • Pietsch EC, Perchiniak E, Canutescu AA et al. Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domain. J Biol Chem. 2008;283(30):21294-304. PubMed
  • Karplus PA, Shapovalov MV, Dunbrack RL, Jr. et al. A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr. 2008;64(Pt 3):335-6. PubMed
  • Shapovalov MV, Dunbrack RL, Jr. Statistical and conformational analysis of the electron density of protein side chains. Proteins. 2007;66(2):279-303. PubMed
  • Shapovalov MV, Canutescu AA, Dunbrack RL, Jr. BioDownloader: Bioinformatics downloads and updates in a few clicks. Bioinformatics. 2007. PubMed
  • Gudima S, Meier A, Dunbrack R et al. Two potentially important elements of the hepatitis B virus large envelope protein are dispensable for the infectivity of hepatitis delta virus. J Virol. 2007;81(8):4343-7. PubMed
  • Dunbrack RLJ. Homology modeling in biology and medicine. In: T Lengauer, editor, translator and editor Bioinformatics: From Genomes to Therapies. Vol. 1. New York: Wiley; 2007; p. 297-349.
  • Xu Q, Canutescu A, Obradovic Z et al. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics. 2006;22(23):2876-82. PubMed
  • Tang Y, Poustovoitov MV, Zhao K et al. Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly. Nat Struct Mol Biol. 2006;13(10):921-9. PubMed
  • Krasley E, Cooper KF, Mallory MJ et al. Regulation of the oxidative stress response through Slt2p-dependent destruction of cyclin C in Saccharomyces cerevisiae. Genetics. 2006;172(3):1477-86. PubMed
  • Dunbrack RL, Jr. Sequence comparison and protein structure prediction. Curr Opin Struct Biol. 2006;16(3):374-84. PubMed
  • Berman HM, Burley SK, Chiu W et al. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006;14(8):1211-7. PubMed
  • Zhang R, Poustovoitov MV, Ye X et al. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell. 2005;8(1):19-30. PubMed
  • Wang G, Sauder JM, Dunbrack Jr RL. Comparative modeling in structural genomics. In: M Sundstrom; M Norin; A Edwards, editors, translator and editor Structural Proteomics and High Throughput Structural Biology. New York: CRC Press; 2005; p. Chapter 7.
  • Wang G, Jin Y, Dunbrack RL, Jr. Assessment of fold recognition predictions in CASP6. Proteins. 2005. PubMed
  • Wang G, Dunbrack RL, Jr. PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res. 2005;33(Web Server issue):W94-8. PubMed
  • Tress M, Tai CH, Wang G et al. Domain definition and target classification for CASP6. Proteins. 2005. PubMed
  • Tarn C, Merkel E, Canutescu AA et al. Analysis of KIT mutations in sporadic and familial gastrointestinal stromal tumors: therapeutic implications through protein modeling. Clin Cancer Res. 2005;11(10):3668-77. PubMed
  • Kahsay RY, Wang G, Gao G et al. Quasi-consensus-based comparison of profile hidden Markov models for protein sequences. Bioinformatics. 2005;21(10):2287-93. PubMed
  • Jin Y, Dunbrack RL, Jr. Assessment of disorder predictions in CASP6. Proteins. 2005;61 Suppl 7:167-75. PubMed
  • Canutescu AA, Dunbrack RL, Jr. MollDE: a homology modeling framework you can click with. Bioinformatics. 2005;21(12):2914-6. PubMed
  • Wang G, Dunbrack RL, Jr. Scoring profile-to-profile sequence alignments. Protein Sci. 2004;13(6):1612-26. PubMed
  • Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics. 2003;19(12):1589-91. PubMed
  • Kundrat L, Martins J, Stith L et al. A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase. J Biol Chem. 2003;278(33):31325-30. PubMed
  • Fischer D, Rychlewski L, Dunbrack RL, Jr. et al. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins. 2003;53 Suppl 6:503-16. PubMed
  • Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 2003;12(9):2001-14. PubMed
  • Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 2003; 12 (5):963-72. PubMed
  • Yi J, Cheng H, Andrake MD et al. Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase. J Biol Chem. 2002;277(14):12164-74. PubMed
  • Prowse AH, Vanderveer L, Milling SW et al. OVCA2 is downregulated and degraded during retinoid-induced apoptosis. Int J Cancer. 2002;99(2):185-92. PubMed
  • Kahsay RY, Wang G, Dongre N et al. CASA: a server for the critical assessment of protein sequence alignment accuracy. Bioinformatics. 2002;18(3):496-7. PubMed
  • Hang H, Zhang Y, Dunbrack RL, Jr. et al. Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1. Genomics. 2002;79(4):487-92. PubMed
  • Grant JD, Dunbrack RL, Manion FJ et al. BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics. 2002;18(5):765-6. PubMed
  • Dunbrack RL, Jr. Rotamer libraries in the 21st century. Curr Opin Struct Biol. 2002;12(4):431-40. PubMed
  • Cheng JD, Dunbrack RL, Jr., Valianou M et al. Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res. 2002;62(16):4767-72. PubMed
  • Shan X, Dunbrack RL, Jr., Christopher SA et al. Mutations in the regulatory domain of cystathionine beta synthase can functionally suppress patient-derived mutations in cis. Hum Mol Genet. 2001;10(6):635-43. PubMed
  • Jaffe EK, Martins J, Li J et al. The molecular mechanism of lead inhibition of human porphobilinogen synthase. J Biol Chem. 2001;276(2):1531-7. PubMed
  • Fischer D, Elofsson A, Rychlewski L et al. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins. 2001;Suppl 5:171-83. PubMed
  • Dunbrack RL, Jr. Protein structure prediction in biology and medicine. In: T Lengauer, editor, translator and editor Bioinformatics and Drug Design. New York: Wiley; 2001.
  • Yi J, Arthur JW, Dunbrack RL, Jr. et al. An inhibitory monoclonal antibody binds at the turn of the helix-turn-helix motif in the N-terminal domain of HIV-1 integrase. J Biol Chem. 2000;275(49):38739-48. PubMed
  • Sauder JM, Dunbrack RL, Jr. Genomic fold assignment and rational modeling of proteins of biological interest. Proc Int Conf Intell Syst Mol Biol. 2000;8:296-306. PubMed
  • Sauder JM, Dunbrack RL, Jr. Beyond genomic fold assignment: Rational modeling of proteins of biological interest. ISMB. 2000;8:296-306.
  • Sauder JM, Arthur JW, Dunbrack RL, Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins. 2000;40(1):6-22. PubMed
  • Sauder JM, Arthur JW, Dunbrack RL, Jr. Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein beta-secretase. J Mol Biol. 2000;300(2):241-8. PubMed
  • Salicioni AM, Xi M, Vanderveer LA et al. Identification and structural analysis of human RBM8A and RBM8B: two highly conserved RNA-binding motif proteins that interact with OVCA1, a candidate tumor suppressor. Genomics. 2000;69(1):54-62. PubMed
  • Kervinen J, Dunbrack RL, Jr., Litwin S et al. Porphobilinogen synthase from pea: expression from an artificial gene, kinetic characterization, and novel implications for subunit interactions. Biochemistry. 2000; 9(30):9018-29. PubMed
  • Jaffe EK, Volin M, Bronson-Mullins CR et al. An artificial gene for human porphobilinogen synthase allows comparison of an allelic variation implicated in susceptibility to lead poisoning. J Biol Chem. 2000; 275(4):2619-26. PubMed
  • Dunbrack RL, Jr., Dunker K, Godzik A. Protein structure prediction in biology and medicine. Pac Symp Biocomput. 2000;(12):93-4. PubMed
  • Dunbrack RL, Jr. Bayesian statistics in structural and molecular biology. In: A MacKerell; M Watanabe; B Roux et al., editors, translator and editor Computational Biochemistry and Biophysics. New York: Marcel Dekker; 2000.
  • Berger MA, Carleton M, Rhodes M et al. Identification of a novel pre-TCR isoform in which the accessibility of the TCR beta subunit is determined by occupancy of the 'missing' V domain of pre-T alpha. Int Immunol. 2000;12(11):1579-91. PubMed

1990 - 1999

  • Zhang YZ, Gould KL, Dunbrack RJ et al. The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily. Physiol Genomics. 1999;1(3):109-18. PubMed
  • Williams M, Lyu MS, Yang YL et al. Ier5, a novel member of the slow-kinetics immediate-early genes. Genomics. 1999;55(3):327-34. PubMed
  • Moraleda G, Seeholzer S, Bichko V et al. Unique properties of the large antigen of hepatitis delta virus. J Virol. 1999;73(9):7147-52. PMIDPubMed
  • Dunbrack RL, Jr. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Proteins. 1999;Suppl 3:81-7. PubMed
  • MacKerell AD, Jr., Bashford D, Bellott M et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem. 1998;B102:3586-616.
  • Dunbrack RL, Jr., Gerloff DL, Bower M et al. Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December. Fold Des. 1997;2(2):R27-42. PubMed
  • Dunbrack RL, Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 1997; 6 (8):1661-81. PubMed
  • Byington CL, Dunbrack RL, Jr., Whitby FG et al. Entamoeba histolytica: computer-assisted modeling of phosphofructokinase for the prediction of broad-spectrum antiparasitic agents. Exp Parasitol. 1997;87(3):194-202. PubMed
  • Byington CL, Dunbrack RL, Jr., Cohen FE et al. Molecular modeling of phosphofructokinase from Entamoeba histolytica for the prediction of new antiparasitic agents. Arch Med Res. 1997;28 Spec No:86-8. PubMed
  • Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol. 1997;267(5):1268-82. PubMed
  • Armand P, Kirshenbaum K, Falicov A et al. Chiral N-substituted glycines can form stable helical conformations. Fold Des. 1997;2(6):369-75. PubMed
  • Dunbrack RL, Jr., Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol. 1994;1(5):334-40. PubMed
  • MacKerell AD, Jr., Bashford D, Bellott M et al. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations. J Phys Chem. 1993;102,(1998):3586-616.
  • Dunbrack RL, Jr., Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol. 1993;230(2):543-74. PubMed
  • Dunbrack RL, Jr. Conformational analysis of protein sidechains: Derivation of empirical energy parameters for proline and development of a backbone-dependent rotamer library [Ph. D. dissertation]: Harvard University; 1993.
  • Shin J, Dunbrack RL, Jr., Lee S et al. Signals for retention of transmembrane proteins in the endoplasmic reticulum studied with CD4 truncation mutants. Proc Natl Acad Sci U S A. 1991;88(5):1918-22. PubMed
  • Shin J, Dunbrack RL, Jr., Lee S et al. Phosphorylation-dependent down-modulation of CD4 requires a specific structure within the cytoplasmic domain of CD4. J Biol Chem. 1991;266(16):10658-65. PubMed

1980 - 1989

  • Doyle C, Shin J, Dunbrack RL, Jr. et al. Mutational analysis of the structure and function of the CD4 protein. Immunol Rev. 1989;109:17-37. PubMed
  • Dunbrack RL, Jr. Calculation of Franck-Condon factors for undergraduate quantum chemistry. J Chem Ed. 1986;63(11):953-5.