Research Topics
Species | R L DunbrackSummaryAffiliation: Fox Chase Cancer Center Country: USA Publications
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Publications
Comparative modeling of CASP3 targets using PSI-BLAST and SCWRLR L Dunbrack
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
Proteins . 1999..SCWRL, which uses a backbone-dependent rotamer library to predict side-chain conformations, did well in comparison with other methods used in CASP3...- 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: ... - 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.... - 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... - An artificial gene for human porphobilinogen synthase allows comparison of an allelic variation implicated in susceptibility to lead poisoningE K Jaffe
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
J Biol Chem 275:2619-26. 2000..However, there was no differential displacement of Zn(II) by Pb(II) between K59 and N59, and simple Pb(II) inhibition studies revealed no allelic difference... - 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... - 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... - 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)... - 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... - 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... - 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.... - 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: 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... - 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... - 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... - Mutations in the regulatory domain of cystathionine beta synthase can functionally suppress patient-derived mutations in cisX Shan
Division of Population Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Hum Mol Genet 10:635-43. 2001..Our results indicate that subtle changes to the C-terminus of CBS can restore activity to mutant proteins and provide a rationale for screening for compounds that can activate mutant CBS alleles... - 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 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... - Genomic fold assignment and rational modeling of proteins of biological interestJ M Sauder
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Proc Int Conf Intell Syst Mol Biol 8:296-306. 2000..Similar results are demonstrated for human disease proteins with known polymorphisms... - Identification and structural analysis of human RBM8A and RBM8B: two highly conserved RNA-binding motif proteins that interact with OVCA1, a candidate tumor suppressorA M Salicioni
Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
Genomics 69:54-62. 2000..The conservation of sequence and structure through such an evolutionarily divergent group of organisms suggests an important function for the RBM8 family of proteins... - 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... - 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.... - 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.... - The molecular mechanism of lead inhibition of human porphobilinogen synthaseE K Jaffe
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
J Biol Chem 276:1531-7. 2001..The data support a novel model where a high affinity lead site is a hybrid of the ZnA and ZnB sites. We propose that the lone electron pair of Pb(II) precludes Pb(II) to function in PBGS catalysis... - BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf clusterJ D Grant
Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Bioinformatics 18:765-6. 2002..The underlying system can also handle automated querying for high throughput work. AVAILABILITY: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/.. - 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... - 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... - 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... - 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... - 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.... - 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... - 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... - Domain definition and target classification for CASP6Michael Tress
Protein Design Group, CNB-CSIC, Calle Darwin, 28049 Cantoblanco, Spain
Proteins 61:8-18. 2005.... - 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... - 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