Paul Bates

Biomolecular Modelling Laboratory

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. 
Computer simulation of a crowded cell interior.

Computer simulation of a crowded cell interior. (Click to view larger image)

Selected publications

Agius R, Torchala, M, Moal, IH, Fernandez-Recio, J, Bates PA. Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organizationPLoS Computational Biology. 2013;9(9):e1003216. 

Tozluoglu M, Tournier AL, Jenkins RP, Hooper S, Bates PA , Sahai, E. Matrix geometry determines optimal cancer migration strategy and modulates response to interventionsNature Cell Biology. 2013; 15:751-762

Cheng TM, Goehring L, Jeffery L, Lu YE, Hayles J, Nov├ík 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 

Cheng, TMK., Agius R, Gulati S, Bates PA. Understanding cancer mechanisms through network dynamicsBrief Funct. Genomics. 2012 (doi: 10.1093/bfgp/els025) 

Moal IH., Bates PA. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. Plos Computational Biology. 2012;8(1):e1002351 

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. 

Moal, IH, Agius, R, Bates, PA. Protein-protein binding affinity prediction on a diverse set of structuresBioinformatics. 2011; 27(21):3002-3009 

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 toxicityBlood. 2011;117(5):1614-21 

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 

 

Paul Bates

Paul Bates

paul.bates@crick.ac.uk
+44 (0)20 379 61762

  • Qualifications and history
  • 1984 PhD in Crystallography, University of Auckland, New Zealand
  • 1984 Postdoctoral Fellow, Queen Mary University, UK
  • 1988 Postdoctoral Fellow, Imperial Cancer Research Fund, UK
  • 2001 Established lab at Imperial Cancer Research Fund, UK (in 2002 the Imperial Cancer Research Fund became Cancer Research UK)
  • 2015 Group Leader, the Francis Crick Institute, London, UK