The London Research Institute research groups are based at Lincoln’s Inn Fields and Clare Hall. Our major research themes are: the biology of tumours and tissues, cellular regulatory mechanisms and genomic integrity and cell cycle.
Paul Bates : Biomolecular Modelling
Goals
In this laboratory we are motivated by fundamental and challenging problems in both structural and systems biology: in particular, how proteins interact at the atomic level to facilitate higher order cellular events. Much of our work involves applying the principles of physics and evolution to the design of novel computer-based algorithms.
Specific areas so far concentrated on are: generating putative protein-protein interaction maps; improving protein structure modelling algorithms; developing algorithms and protocols to predict flexible protein-ligand complex formation; predict binding affinities; modelling of protein networks coupled to cell patterning such as found in early angiogenesis - new blood vessel formation - and cancer cell motility; modelling system level dynamic effects of nonsynonymous single nucleotide polymorphisms (SNPs) within key cellular pathways.
Selected Papers
Cheng TM, Goehring L, Jeffery L, Lu YE, Hayles J, Novák B, Bates PA. A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Computational Biology. 2012;8(10):e1002738
(Abstract)
Cheng, TMK., Agius R, Gulati S, Bates PA. Understanding cancer mechanisms through network dynamics. Brief Funct. Genomics. 2012 (doi: 10.1093/bfgp/els025)
(Abstract)
Moal IH., Bates PA. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. Plos Computational Biology. 2012;8(1):e1002351
(Abstract)
Torchala M, Chelminiak P, Bates PA. Mean first-passage time calculations comparison of the deterministic Hill’s algorithm with Monte Carlo simulations. Eur. Phys. J. B. 2012; 85(4), 116.
Fleishman, S.J., Whitehead, T.A., Strauch, E.M., Corn, J.E., Qin, S., Zhou, H.X., Mitchell, J.C., Demerdash, O.N.A., Takeda-Shitaka, M., Terashi, G., Moal, I.H., Li, X., Bates, P.A., Zacharias, M., Park, H., Ko., J.S., Lee, H., Seok, C., Bourguard, T., Bernauer, J., Poupon, A., Aze, J., Soner, S., Ovali, S.K., Ozbek, P., Tal, N.B., Holiloglu, T., Hwang, H., Vreven, T., Pierce, B.G., Weng, Z., Perez-Cano, L., Pons, C., Fernandez-Recio, J., Jiang, F., Yang, F., Gong, X., Cao, L., Xu, X., Liu, B., Wang, P., Li, C., Wang, C., Robert, C.H., Guharoy, M., Liu, S., Huang, Y., Li, L., Guo, D., Chen, Y., Xiao, Y., London, N., Itzhaki, Z., Schueler-Furman, O., Ibar, Y., Patapov, V., Cohen, M., Schreiber, G., Tsuchiva, Y., Kanamori, E., Standley, D.M., Nakamura, H., Kinoshita, K., Driggers, C.M., Hall, R.G., Morgan, J.L., Hsu, V.L., Zhan, J., Yang, Y., Zhou, Y., Kastritis, P.L., Bonvin, A.M.J.J., Zhang, W., Camacho, C.J., Kilambi, K.P., Sircar, A., Gray, J.J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, Y., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodriguez, J., Kihara, D., Stranges, P.B., Jacak, R., Kuhlman, B., Sheng-Huang, Zou, X., Wodak, S.J., Janin, J. & Baker, D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J. Mol. Biol. 2011;414(2):289-302.
(Abstract)
Moal, IH, Agius, R, Bates, PA. Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics. 2011; 27(21):3002-3009
(Abstract)
Offman MN, Krol M, Patel N, Krishnan S, Liu J, Saha V, Bates PA. Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity. Blood. 2011;117(5):1614-21
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Li X, Moal IH, Bates PA. Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins. 2010;78(15):3189–96
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Bentley K, Mariggi G, Gerhardt H, Bates PA. Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis. Plos Computational Biology. 2009;5(10):e1000549
(Abstract)
Jonsson PF, Bates PA. Global topological features of cancer proteins in the human interactome. Bioinformatics. 2006;22:2291-2297
(Abstract)
Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol. 2005;347:1077-1101
(Abstract)
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Paul Bates
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