Roland Dunbrack

Summary

Affiliation: Fox Chase Cancer Center
Country: USA

Publications

  1. ncbi request reprint Assessment of disorder predictions in CASP6
    Yumi Jin
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Proteins 61:167-75. 2005
  2. pmc PISCES: recent improvements to a PDB sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Nucleic Acids Res 33:W94-8. 2005
  3. pmc The role of balanced training and testing data sets for binary classifiers in bioinformatics
    Qiong Wei
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e67863. 2013
  4. pmc The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite
    Jared Adolf-Bryfogle
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e66856. 2013
  5. pmc The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms
    Qifang Xu
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Nucleic Acids Res 39:D761-70. 2011
  6. pmc Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model
    Daniel Ting
    Department of Statistics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 6:e1000763. 2010
  7. ncbi request reprint Sequence comparison and protein structure prediction
    Roland L Dunbrack
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Curr Opin Struct Biol 16:374-84. 2006
  8. ncbi request reprint ProtBuD: a database of biological unit structures of protein families and superfamilies
    Qifang Xu
    Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111 USA
    Bioinformatics 22:2876-82. 2006
  9. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
  10. ncbi request reprint Assessment of fold recognition predictions in CASP6
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Proteins 61:46-66. 2005

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Assessment of disorder predictions in CASP6
    Yumi Jin
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Proteins 61:167-75. 2005
    ..Several groups performed quite well in predicting regions of disorder in the X-ray and NMR structures available to the assessors. The best of these groups performed better than the best groups in CASP5, held in 2002...
  2. pmc PISCES: recent improvements to a PDB sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Nucleic Acids Res 33:W94-8. 2005
    ..The server's data are updated weekly. The server is available at http://dunbrack.fccc.edu/pisces...
  3. pmc The role of balanced training and testing data sets for binary classifiers in bioinformatics
    Qiong Wei
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e67863. 2013
    ..The appropriate approach depends on the amount of available data and the specific problem at hand. ..
  4. pmc The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite
    Jared Adolf-Bryfogle
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e66856. 2013
    ..The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI. ..
  5. pmc The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms
    Qifang Xu
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Nucleic Acids Res 39:D761-70. 2011
    ..Common interfaces may also be useful in studies of protein evolution. Coordinates for all interfaces in a cluster are downloadable for further analysis. ProtCiD is available at http://dunbrack2.fccc.edu/protcid...
  6. pmc Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model
    Daniel Ting
    Department of Statistics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 6:e1000763. 2010
    ..The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp...
  7. ncbi request reprint Sequence comparison and protein structure prediction
    Roland L Dunbrack
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Curr Opin Struct Biol 16:374-84. 2006
    ....
  8. ncbi request reprint ProtBuD: a database of biological unit structures of protein families and superfamilies
    Qifang Xu
    Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111 USA
    Bioinformatics 22:2876-82. 2006
    ..It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs...
  9. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
    ..The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs...
  10. ncbi request reprint Assessment of fold recognition predictions in CASP6
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Proteins 61:46-66. 2005
    ..The top-ranked methods in prediction of structures less clearly related or unrelated to proteins of known structures used fragment building methods in addition to the fold recognition meta methods...
  11. pmc SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
    Qiang Wang
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Nat Protoc 3:1832-47. 2008
    ..SCWRL and MolIDE can be obtained at (http://dunbrack.fccc.edu/Software.php)...
  12. ncbi request reprint PISCES: a protein sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 19:1589-91. 2003
    ..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
  13. pmc A graph-theory algorithm for rapid protein side-chain prediction
    Adrian A Canutescu
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Protein Sci 12:2001-14. 2003
    ....
  14. ncbi request reprint OVCA2 is downregulated and degraded during retinoid-induced apoptosis
    Amanda H Prowse
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Int J Cancer 99:185-92. 2002
    ..Our results are in contrast to a previous report and show that OVCA2, not OVCA1 mRNA and protein, is downregulated in response to RA and 4HPR...
  15. ncbi request reprint Rotamer libraries in the 21st century
    Roland L Dunbrack
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia PA 19111, USA
    Curr Opin Struct Biol 12:431-40. 2002
    ....
  16. ncbi request reprint Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model
    Jonathan D Cheng
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Cancer Res 62:4767-72. 2002
    ..Moreover, tumor growth is attenuated by antibodies that inhibit the proteolytic activity of FAP. These findings suggest a possible therapeutic role for functional inhibition of FAP activity...
  17. ncbi request reprint MollDE: a homology modeling framework you can click with
    Adrian A Canutescu
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 21:2914-6. 2005
    ..MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE...
  18. pmc Cyclic coordinate descent: A robotics algorithm for protein loop closure
    Adrian A Canutescu
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Protein Sci 12:963-72. 2003
    ..It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average...
  19. pmc Statistical analysis of interface similarity in crystals of homologous proteins
    Qifang Xu
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    J Mol Biol 381:487-507. 2008
    ..The PDB, in particular, is missing highly likely biological interfaces in its biological unit files for about 10% of PDB entries...
  20. pmc Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase
    Qiong Wei
    Program in Molecular and Translational Medicine, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 78:2058-74. 2010
    ....
  21. ncbi request reprint Statistical and conformational analysis of the electron density of protein side chains
    Maxim V Shapovalov
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Proteins 66:279-303. 2007
    ..These results indicate that modeling of side chains alternating between rotamers in the electron density is important and needs further improvement, both in structure determination and in structure prediction...
  22. pmc Scoring profile-to-profile sequence alignments
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Protein Sci 13:1612-26. 2004
    ....
  23. pmc An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases
    Brian Weitzner
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 75:289-95. 2009
    ..Even crystal structures of mouse SULT1E1, which is a monomer in solution, contain the common dimeric interface, although distorted and missing two important salt bridges...
  24. pmc Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domain
    E Christine Pietsch
    Division of Medical Sciences and Program in Biomolecular Structure and Function, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    J Biol Chem 283:21294-304. 2008
    ..The combined data point to the H2 helix and L1 and L3 loops of p53 as novel functional domains contributing to transcription-independent apoptosis by this tumor suppressor protein...
  25. ncbi request reprint Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA
    Rugang Zhang
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Dev Cell 8:19-30. 2005
    ..These data indicate that HIRA and ASF1a drive formation of macroH2A-containing SAHF and senescence-associated cell cycle exit, via a pathway that appears to depend on flux of heterochromatic proteins through PML bodies...
  26. pmc Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation
    Paschalis Thomas Doulias
    Children s Hospital of Philadelphia Research Institute and Department of Pharmacology, Children s Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 107:16958-63. 2010
    ..Collectively, the endogenous S-nitrosoproteome in the liver has structural features that accommodate multiple mechanisms for selective site-directed S-nitrosylation...
  27. ncbi request reprint A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase
    Lenka Kundrat
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 2497, USA
    J Biol Chem 278:31325-30. 2003
    ..5/subunit. This result reveals a structural basis for half-of-the-sites metal binding that is consistent with a reciprocating motion model for function of oligomeric PBGS...
  28. ncbi request reprint Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase
    Jizu Yi
    Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, Pennsylvania 19111, USA
    J Biol Chem 277:12164-74. 2002
    ....
  29. ncbi request reprint BioDownloader: bioinformatics downloads and updates in a few clicks
    Maxim V Shapovalov
    Fox Chase Cancer Center, Philadelphia PA 19111 USA
    Bioinformatics 23:1437-9. 2007
    ..AVAILABILITY: The program can be installed from http://dunbrack.fccc.edu/BioDownloader. The software is freely available for both non-commercial and commercial users under the BSD license...
  30. ncbi request reprint Domain definition and target classification for CASP6
    Michael Tress
    Protein Design Group, CNB CSIC, Calle Darwin, 28049 Cantoblanco, Spain
    Proteins 61:8-18. 2005
    ....
  31. ncbi request reprint CAFASP3: the third critical assessment of fully automated structure prediction methods
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:503-16. 2003
    ..This result shows that significant progress has been achieved in automatic structure prediction and has important implications to the prospects of automated structure modeling in the context of structural genomics...
  32. ncbi request reprint CASA: a server for the critical assessment of protein sequence alignment accuracy
    Robel Y Kahsay
    Delaware Biotechnology Institute and Department of Electrical and Computer Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
    Bioinformatics 18:496-7. 2002
    ..The server produces graphical and tabular comparisons of the accuracy of a user's input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99...
  33. ncbi request reprint Outcome of a workshop on archiving structural models of biological macromolecules
    Helen M Berman
    The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
    Structure 14:1211-7. 2006
  34. ncbi request reprint Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1
    Haiying Hang
    Center for Radiological Research, Columbia University, 630 West 168th Street, New York, New York 10032, USA
    Genomics 79:487-92. 2002
    ..Furthermore, overexpression of HUS1B but not HUS1 in human cells induces clonogenic cell death. We suggest that HUS1B and HUS1 have distinct but related roles in regulating cell cycle checkpoints and genomic integrity...

Research Grants14

  1. New Methods for High-Resolution Comparative Modeling
    Roland Dunbrack; Fiscal Year: 2007
    ..New structures from three Protein Structure Initiative centers will be used both as prediction targets (before they are solved) and as templates for prediction of structures of important biological or clinical interest. ..
  2. Modeling of Protein Complexes and Missense Mutations
    Roland Dunbrack; Fiscal Year: 2007
    ..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
  3. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2002
    ..The increase in size of the sequence and structure databases makes the new statistical analysis timely, both because of the increased power the new data provide, and the numerous applications afforded by more sequences and structures. ..
  4. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2009
    ..These methods will be used to improve human health through the prediction of proteins involved in disease. ..
  5. Modeling of Protein Complexes and Missense Mutations
    Roland Dunbrack; Fiscal Year: 2009
    ..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
  6. Modeling of Protein Complexes and Missense Mutations
    Roland Dunbrack; Fiscal Year: 2006
    ..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
  7. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2006
    ..The increase in size of the sequence and structure databases makes the new statistical analysis timely, both because of the increased power the new data provide, and the numerous applications afforded by more sequences and structures. ..
  8. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2005
    ..The increase in size of the sequence and structure databases makes the new statistical analysis timely, both because of the increased power the new data provide, and the numerous applications afforded by more sequences and structures. ..
  9. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2004
    ..The increase in size of the sequence and structure databases makes the new statistical analysis timely, both because of the increased power the new data provide, and the numerous applications afforded by more sequences and structures. ..
  10. Bayesian Statistics and Algorithms for Homology Modeling
    Roland Dunbrack; Fiscal Year: 2003
    ..The increase in size of the sequence and structure databases makes the new statistical analysis timely, both because of the increased power the new data provide, and the numerous applications afforded by more sequences and structures. ..
  11. Bayesian Statistics and Algorithms for Homology Modeling
    Roland L Dunbrack; Fiscal Year: 2010
    ..These methods will be used to improve human health through the prediction of proteins involved in disease. ..