Paul Bates: Publications

  • Moal, IH; Barradas-Bautista, D; Jiménez-García, B; Torchala, M; van der Velde, A; Vreven, T; Weng, Z; Bates, PA and Fernández-Recio, J (2017)
    IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
    Bioinformatics 33, 1806-1813 PubMed abstract
  • Pfeiffenberger, E; Chaleil, RAG; Moal, I and Bates, PA (2017)
    A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.
    Proteins 85, 528-543 PubMed abstract
  • Law, TR; Hancox, J; Cheng, TMK; Chaleil, RAG; Wright, SA; Bates, PA; Jarvis, SA and IEEE (2016)
    Optimisation of a molecular dynamics simulation of chromosome condensation.
    In: Proceedings of 28th IEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD).
    2016. 126-133. (International Symposium on Computer Architecture and High Performance Computing).
  • Lensink, MF; Velankar, S; Kryshtafovych, A; Huang, S-Y; Schneidman-Duhovny, D; Sali, A; Segura, J; Fernandez-Fuentes, N; Viswanath, S; Elber, R; Grudinin, S; Popov, P; Neveu, E; Lee, H; Baek, M; Park, S; Heo, L; Rie Lee, G; Seok, C; Qin, S; Zhou, H-X; Ritchie, DW; Maigret, B; Devignes, M-D; Ghoorah, A; Torchala, M; Chaleil, RAG; Bates, PA; Ben-Zeev, E; Eisenstein, M; Negi, SS; Weng, Z; Vreven, T; Pierce, BG; Borrman, TM; Yu, J; Ochsenbein, F; Guerois, R; Vangone, A; Rodrigues, JPGLM; van Zundert, G; Nellen, M; Xue, L; Karaca, E; Melquiond, ASJ; Visscher, K; Kastritis, PL; Bonvin, AMJJ; Xu, X; Qiu, L; Yan, C; Li, J; Ma, Z; Cheng, J; Zou, X; Shen, Y; Peterson, LX; Kim, H-R; Roy, A; Han, X; Esquivel-Rodriguez, J; Kihara, D; Yu, X; Bruce, NJ; Fuller, JC; Wade, RC; Anishchenko, I; Kundrotas, PJ; Vakser, IA; Imai, K; Yamada, K; Oda, T; Nakamura, T; Tomii, K; Pallara, C; Romero-Durana, M; Jiménez-García, B; Moal, IH; Férnandez-Recio, J; Joung, JY; Kim, JY; Joo, K; Lee, J; Kozakov, D; Vajda, S; Mottarella, S; Hall, DR; Beglov, D; Mamonov, A; Xia, B; Bohnuud, T; Del Carpio, CA; Ichiishi, E; Marze, N; Kuroda, D; Roy Burman, SS; Gray, JJ; Chermak, E; Cavallo, L; Oliva, R; Tovchigrechko, A and Wodak, SJ (2016)
    Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
    Proteins 84, 323-348 PubMed abstract
  • Mylona, A; Theillet, F-X; Foster, C; Cheng, TM; Miralles, F; Bates, PA; Selenko, P and Treisman, R (2016)
    Opposing effects of Elk-1 multisite phosphorylation shape its response to ERK activation.
    Science 354, 233-237 PubMed abstract
  • Samora, CP; Saksouk, J; Goswami, P; Wade, BO; Singleton, MR; Bates, PA; Lengronne, A; Costa, A and Uhlmann, F (2016)
    Ctf4 links DNA replication with sister chromatid cohesion establishment by recruiting the Chl1 helicase to the replisome.
    Molecular Cell 63, 371-384 PubMed abstract
  • Bush, M; Ghosh, T; Sawicka, M; Moal, IH; Bates, PA; Dixon, R and Zhang, X (2015)
    The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.
    Molecular Microbiology 95, 17-30 PubMed abstract
  • Cheng, TMK; Heeger, S; Chaleil, RAG; Matthews, N; Stewart, A; Wright, J; Lim, C; Bates, PA and Uhlmann, F (2015)
    A simple biophysical model emulates budding yeast chromosome condensation.
    eLife 4, e05565 PubMed abstract
  • Gulati, S; Turajlic, S; Larkin, J; Bates, PA and Swanton, C (2015)
    Relapse models for clear cell renal carcinoma.
    Lancet Oncology 16, e376-e378 PubMed abstract
  • Kanu, N; Grönroos, E; Martinez, P; Burrell, RA; Yi Goh, X; Bartkova, J; Maya-Mendoza, A; Mistrik, M; Rowan, AJ; Patel, H; Rabinowitz, A; East, P; Wilson, G; Santos, CR; McGranahan, N; Gulati, S; Gerlinger, M; Birkbak, NJ; Joshi, T; Alexandrov, LB; Stratton, MR; Powles, T; Matthews, N; Bates, PA; Stewart, A; Szallasi, Z; Larkin, J; Bartek, J and Swanton, C (2015)
    SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.
    Oncogene 34, 5699-5708 PubMed abstract
  • Madsen, CD; Hooper, S; Tozluoglu, M; Bruckbauer, A; Fletcher, G; Erler, JT; Bates, PA; Thompson, B and Sahai, E (2015)
    STRIPAK components determine mode of cancer cell migration and metastasis.
    Nature Cell Biology 17, 68-80 PubMed abstract
  • Tozluoglu, M; Mao, Y; Bates, PA and Sahai, E (2015)
    Cost-benefit analysis of the mechanisms that enable migrating cells to sustain motility upon changes in matrix environments.
    Journal of the Royal Society Interface 12, 20141355 PubMed abstract
  • Vreven, T; Moal, IH; Vangone, A; Pierce, BG; Kastritis, PL; Torchala, M; Chaleil, R; Jiménez-García, B; Bates, PA; Fernandez-Recio, J; Bonvin, AMJJ and Weng, Z (2015)
    Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2.
    Journal of Molecular Biology 427, 3031-3041 PubMed abstract
  • Fisher, R; Horswell, S; Rowan, A; Salm, MP; de Bruin, EC; Gulati, S; McGranahan, N; Stares, M; Gerlinger, M; Varela, I; Crockford, A; Favero, F; Quidville, V; André, F; Navas, C; Grönroos, E; Nicol, D; Hazell, S; Hrouda, D; O'Brien, T; Matthews, N; Phillimore, B; Begum, S; Rabinowitz, A; Biggs, J; Bates, PA; McDonald, NQ; Stamp, G; Spencer-Dene, B; Hsieh, JJ; Xu, J; Pickering, L; Gore, M; Larkin, J and Swanton, C (2014)
    Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution.
    Genome Biology 15, 433 PubMed abstract
  • Gerlinger, M; Horswell, S; Larkin, J; Rowan, AJ; Salm, MP; Varela, I; Fisher, R; McGranahan, N; Matthews, N; Santos, CR; Martinez, P; Phillimore, B; Begum, S; Rabinowitz, A; Spencer-Dene, B; Gulati, S; Bates, PA; Stamp, G; Pickering, L; Gore, M; Nicol, DL; Hazell, S; Futreal, PA; Stewart, A and Swanton, C (2014)
    Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing.
    Nature Genetics 46, 225-233 PubMed abstract
  • Gulati, S; Martinez, P; Joshi, T; Birkbak, NJ; Santos, CR; Rowan, AJ; Pickering, L; Gore, M; Larkin, J; Szallasi, Z; Bates, PA; Swanton, C and Gerlinger, M (2014)
    Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers.
    European Urology 66, 936-948 PubMed abstract
  • Lensink, MF; Moal, IH; Bates, PA; Kastritis, PL; Melquiond, ASJ; Karaca, E; Schmitz, C; van Dijk, M; Bonvin, AMJJ; Eisenstein, M; Jiménez-García, B; Grosdidier, S; Solernou, A; Pérez-Cano, L; Pallara, C; Fernández-Recio, J; Xu, J; Muthu, P; Praneeth Kilambi, K; Gray, JJ; Grudinin, S; Derevyanko, G; Mitchell, JC; Wieting, J; Kanamori, E; Tsuchiya, Y; Murakami, Y; Sarmiento, J; Standley, DM; Shirota, M; Kinoshita, K; Nakamura, H; Chavent, M; Ritchie, DW; Park, H; Ko, J; Lee, H; Seok, C; Shen, Y; Kozakov, D; Vajda, S; Kundrotas, PJ; Vakser, IA; Pierce, BG; Hwang, H; Vreven, T; Weng, Z; Buch, I; Farkash, E; Wolfson, HJ; Zacharias, M; Qin, S; Zhou, H-X; Huang, S-Y; Zou, X; Wojdyla, JA; Kleanthous, C and Wodak, SJ (2014)
    Blind prediction of interfacial water positions in CAPRI.
    Proteins 82, 620-632 PubMed abstract
  • Torchala, M and Bates, PA (2014)
    Predicting the structure of protein-protein complexes using the SwarmDock Web Server.
    Methods in Molecular Biology 1137, 181-197 PubMed abstract
  • Agius, R; Torchala, M; Moal, IH; Fernández-Recio, J and Bates, PA (2013)
    Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.
    PLOS Computational Biology 9, e1003216 PubMed abstract
  • Gulati, S; Cheng, TMK and Bates, PA (2013)
    Cancer networks and beyond: interpreting mutations using the human interactome and protein structure.
    Seminars in Cancer Biology 23, 219-226 PubMed abstract
  • Moal, IH; Torchala, M; Bates, PA and Fernández-Recio, J (2013)
    The scoring of poses in protein-protein docking: current capabilities and future directions.
    BMC Bioinformatics 14, 286 PubMed abstract
  • Moretti, R; Fleishman, SJ; Agius, R; Torchala, M; Bates, PA; Kastritis, PL; Rodrigues, JPGLM; Trellet, M; Bonvin, AMJJ; Cui, M; Rooman, M; Gillis, D; Dehouck, Y; Moal, I; Romero-Durana, M; Perez-Cano, L; Pallara, C; Jimenez, B; Fernandez-Recio, J; Flores, S; Pacella, M; Praneeth Kilambi, K; Gray, JJ; Popov, P; Grudinin, S; Esquivel-Rodríguez, J; Kihara, D; Zhao, N; Korkin, D; Zhu, X; Demerdash, ONA; Mitchell, JC; Kanamori, E; Tsuchiya, Y; Nakamura, H; Lee, H; Park, H; Seok, C; Sarmiento, J; Liang, S; Teraguchi, S; Standley, DM; Shimoyama, H; Terashi, G; Takeda-Shitaka, M; Iwadate, M; Umeyama, H; Beglov, D; Hall, DR; Kozakov, D; Vajda, S; Pierce, BG; Hwang, H; Vreven, T; Weng, Z; Huang, Y; Li, H; Yang, X; Ji, X; Liu, S; Xiao, Y; Zacharias, M; Qin, S; Zhou, H-X; Huang, S-Y; Zou, X; Velankar, S; Janin, J; Wodak, SJ and Baker, D (2013)
    Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
    Proteins 81, 1980-1987 PubMed abstract
  • Torchala, M; Chelminiak, P; Kurzynski, M and Bates, PA (2013)
    RaTrav: a tool for calculating mean first-passage times on biochemical networks.
    BMC Systems Biology 7, 130 PubMed abstract
  • Torchala, M; Moal, IH; Chaleil, RAG; Agius, R and Bates, PA (2013)
    A Markov-chain model description of binding funnels to enhance the ranking of docked solutions.
    Proteins 81, 2143-2149 PubMed abstract
  • Torchala, M; Moal, IH; Chaleil, RAG; Fernandez-Recio, J and Bates, PA (2013)
    SwarmDock: a server for flexible protein-protein docking.
    Bioinformatics 29, 807-809 PubMed abstract
  • Tozluoğlu, M; Tournier, AL; Jenkins, RP; Hooper, S; Bates, PA and Sahai, E (2013)
    Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions.
    Nature Cell Biology 15, 751-762 PubMed abstract
  • Zhou, H-X and Bates, PA (2013)
    Modeling protein association mechanisms and kinetics.
    Current Opinion in Structural Biology 23, 887-893 PubMed abstract
  • Cheng, TMK; Goehring, L; Jeffery, L; Lu, Y-E; Hayles, J; Novák, B and Bates, PA (2012)
    A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins.
    PLOS Computational Biology 8, e1002738 PubMed abstract
  • Cheng, TMK; Gulati, S; Agius, R and Bates, PA (2012)
    Understanding cancer mechanisms through network dynamics.
    Briefings in Functional Genomics 11, 543-560 PubMed abstract
  • Moal, IH and Bates, PA (2012)
    Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.
    PLOS Computational Biology 8, e1002351 PubMed abstract
  • Torchala, M; Chelminiak, P and Bates, PA (2012)
    Mean first-passage time calculations: comparison of the deterministic Hill's algorithm with Monte Carlo simulations.
    European Physical Journal B 85, 116
  • Fleishman, SJ; Whitehead, TA; Strauch, E-M; Corn, JE; Qin, S; Zhou, H-X; Mitchell, JC; Demerdash, ONA; Takeda-Shitaka, M; Terashi, G; Moal, IH; Li, X; Bates, PA; Zacharias, M; Park, H; Ko, J-s; Lee, H; Seok, C; Bourquard, T; Bernauer, J; Poupon, A; Azé, J; Soner, S; Ovalı, ŞK; Ozbek, P; Tal, NB; Haliloglu, T; Hwang, H; Vreven, T; Pierce, BG; Weng, Z; Peréz-Cano, L; Pons, C; Fernández-Recio, J; Jiang, F; Yang, F; Gong, X; Cao, L; Xu, X; Liu, B; Wang, P; Li, C; Wang, C; Robert, CH; Guharoy, M; Liu, S; Huang, Y; Li, L; Guo, D; Chen, Y; Xiao, Y; London, N; Itzhaki, Z; Schueler-Furman, O; Inbar, Y; Potapov, V; Cohen, M; Schreiber, G; Tsuchiya, Y; Kanamori, E; Standley, DM; Nakamura, H; Kinoshita, K; Driggers, CM; Hall, RG; Morgan, JL; Hsu, VL; Zhan, J; Yang, Y; Zhou, Y; Kastritis, PL; Bonvin, AMJJ; Zhang, W; Camacho, CJ; Kilambi, KP; Sircar, A; Gray, JJ; Ohue, M; Uchikoga, N; Matsuzaki, Y; Ishida, T; Akiyama, Y; Khashan, R; Bush, S; Fouches, D; Tropsha, A; Esquivel-Rodríguez, J; Kihara, D; Stranges, PB; Jacak, R; Kuhlman, B; Huang, S-Y; Zou, X; Wodak, SJ; Janin, J and Baker, D (2011)
    Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
    Journal of Molecular Biology 414, 289-302 PubMed abstract
  • Kastritis, PL; Moal, IH; Hwang, H; Weng, Z; Bates, PA; Bonvin, AMJJ and Janin, J (2011)
    A structure-based benchmark for protein-protein binding affinity.
    Protein Science 20, 482-491 PubMed abstract
  • Lara, R; Mauri, FA; Taylor, H; Derua, R; Shia, A; Gray, C; Nicols, A; Shiner, RJ; Schofield, E; Bates, PA; Waelkens, E; Dallman, M; Lamb, J; Zicha, D; Downward, J; Seckl, MJ and Pardo, OE (2011)
    An siRNA screen identifies RSK1 as a key modulator of lung cancer metastasis.
    Oncogene 30, 3513-3521 PubMed abstract
  • Mao, Y; Tournier, AL; Bates, PA; Gale, JE; Tapon, N and Thompson, BJ (2011)
    Planar polarization of the atypical myosin Dachs orients cell divisions in Drosophila.
    Genes & Development 25, 131-136 PubMed abstract
  • Moal, IH; Agius, R and Bates, PA (2011)
    Protein-protein binding affinity prediction on a diverse set of structures.
    Bioinformatics 27, 3002-3009 PubMed abstract
  • Offman, MN; Krol, M; Patel, N; Krishnan, S; Liu, J; Saha, V and Bates, PA (2011)
    Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity.
    Blood 117, 1614-1621 PubMed abstract
  • Kurkcuoglu, O and Bates, PA (2010)
    Mechanism of cohesin loading onto chromosomes: a conformational dynamics study.
    Biophysical Journal 99, 1212-1220 PubMed abstract
  • Li, X; Moal, I and Bates, P (2010)
    Bridging the gaps: atomic simulation of macromolecular environment brings together protein docking, interaction kinetics and the crowding effects.
    BMC Bioinformatics 11, O2
  • Li, X; Moal, IH and Bates, PA (2010)
    Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding.
    Proteins 78, 3189-3196 PubMed abstract
  • Moal, IH and Bates, PA (2010)
    SwarmDock and the use of normal modes in protein-protein docking.
    International Journal of Molecular Sciences 11, 3623-3648 PubMed abstract

[Page last updated 1 Nov 2017]

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