Roland L Dunbrack, Jr, PhD
Office Phone: 215-728-2434
The Dunbrack group concentrates on research in computational structural biology, including homology modeling, fold recognition, molecular dynamics simulations, statistical analysis of the PDB, and bioinformatics. In developing these methods, we use methods from various areas of mathematics and computer science, including Bayesian statistics and computational geometry. We place an emphasis on large-scale benchmarking of new methods and comparison with existing methods. We are interested in applying comparative modeling to important problems in various areas of biology. Areas of particular interest include DNA repair, proteases and other peptide-binding protein families, and membrane proteins.
Our software development uses visual programming environments, such as Visual Studio, and modern programming languages such as object-oriented C++ and C#. Our goal is to produce easy-to-use, professional software for use in our own research as well as to be distributed to other research groups around the world.
Description of research projects
Fox Chase Programs
- 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
- Wang Q, Canutescu AA, Dunbrack RL Jr. SCWRL and MollDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc. 2008;3:1832-47. PubMed
- Xu Q, Canutescu AA, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL Jr. Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol. 2008;381:487-507. PubMed
- Shapovalov MV, Dunbrack RL Jr. Statistical and conformational analysis of the electron density of protein side chains. Proteins. 2007;66:279-303. PubMed
- Xu Q, Canutescu A, Obradvic Z, Dunbrack RL Jr. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics 2006;22:2876-82. PubMed
- Wang G, Dunbrack RL Jr. PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res. 33:W94-W98, 2005. PubMed