Research Topics
Species | Roland DunbrackSummaryAffiliation: Fox Chase Cancer Center Country: USA Publications
Research Grants
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Detail Information
Publications
Assessment of disorder predictions in CASP6Yumi 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...- Sequence comparison and protein structure predictionRoland 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.... - PISCES: a protein sequence culling serverGuoli 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... 
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modelingQiang 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)...- Assessment of fold recognition predictions in CASP6Guoli 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... - Improved prediction of protein side-chain conformations with SCWRL4Georgii 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... - ProtBuD: a database of biological unit structures of protein families and superfamiliesQifang Xu
Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111 USA
Bioinformatics 22:2876-82. 2006..AVAILABILITY: The database is provided as a standalone program and a web server from http://dunbrack.fccc.edu/ProtBuD.php... - A graph-theory algorithm for rapid protein side-chain predictionAdrian A Canutescu
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
Protein Sci 12:2001-14. 2003.... - Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal modelJonathan 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... - Rotamer libraries in the 21st centuryRoland 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.... - OVCA2 is downregulated and degraded during retinoid-induced apoptosisAmanda 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... - MollDE: a homology modeling framework you can click withAdrian A Canutescu
Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
Bioinformatics 21:2914-6. 2005..This allows developers to integrate additional third-party programs to MolIDE. AVAILABILITY: http://dunbrack.fccc.edu/molide/molide.php CONTACT: ... - PISCES: recent improvements to a PDB sequence culling serverGuoli 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... - Statistical analysis of interface similarity in crystals of homologous proteinsQifang 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... - Cyclic coordinate descent: A robotics algorithm for protein loop closureAdrian 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... - Statistical and conformational analysis of the electron density of protein side chainsMaxim 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... - Scoring profile-to-profile sequence alignmentsGuoli Wang
Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
Protein Sci 13:1612-26. 2004.... - Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthaseQiong Wei
Program in Molecular and Translational Medicine, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
Proteins 78:2058-74. 2010.... - Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRARugang 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... - An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferasesBrian 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... - Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domainE 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... - Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integraseJizu Yi
Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, Pennsylvania 19111, USA
J Biol Chem 277:12164-74. 2002.... - Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylationPaschalis 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... - A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthaseLenka 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... - BioDownloader: bioinformatics downloads and updates in a few clicksMaxim 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... - CAFASP3: the third critical assessment of fully automated structure prediction methodsDaniel 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... - CASA: a server for the critical assessment of protein sequence alignment accuracyRobel 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..AVAILABILITY: The server is located at http://capb.dbi.udel.edu/casa... - Domain definition and target classification for CASP6Michael Tress
Protein Design Group, CNB-CSIC, Calle Darwin, 28049 Cantoblanco, Spain
Proteins 61:8-18. 2005.... - Outcome of a workshop on archiving structural models of biological macromoleculesHelen 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 - Identification and characterization of a paralog of human cell cycle checkpoint gene HUS1Haiying 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 Grants
- New Methods for High-Resolution Comparative ModelingRoland 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. ..
- Bayesian Statistics and Algorithms for Homology ModelingRoland Dunbrack; Fiscal Year: 2009..These methods will be used to improve human health through the prediction of proteins involved in disease. ..
- Modeling of Protein Complexes and Missense MutationsRoland Dunbrack; Fiscal Year: 2009..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
- Modeling of Protein Complexes and Missense MutationsRoland Dunbrack; Fiscal Year: 2007..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
- Bayesian Statistics and Algorithms for Homology ModelingRoland 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. ..
- Bayesian Statistics and Algorithms for Homology ModelingRoland L Dunbrack; Fiscal Year: 2010..These methods will be used to improve human health through the prediction of proteins involved in disease. ..