Leo Caves

Search results

• 2019

  Thinking (in) complexity: (In) definitions and (mis)conceptions

  Teixeira de Melo, A., Caves, L. S. D., Dewitt, A., Clutton, E., Macpherson, R. & Garnett, P., 22 Jul 2019, (E-pub ahead of print) In: Systems Research and Behavioral Science. 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2017

  Artificial Epigenetic Networks: Automatic Decomposition of Dynamical Control Tasks using Topological Self-Modification

  Turner, A. P., Caves, L., Stepney, S., Tyrrell, A. & Lones, M. A., Jan 2017, In: IEEE transactions on neural networks and learning systems . 28, 1, p. 218-230 13 p., 7372471.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2016

  Recognition Dynamics of p53 and MDM2: Implications for Peptide Design

  Elsawy, K. M., Lane, D. P., Verma, C. S. & Caves, L. S. D., 21 Jan 2016, In: Journal of Physical Chemistry B. 120, 2, p. 320-328 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2015

  A spatiotemporal characterization of the effect of p53 phosphorylation on its interaction with MDM2

  ElSawy, K. M., Sim, A., Lane, D. P., Verma, C. S. & Caves, L. S. D., 2015, In: Cell cycle. 14, 2, p. 179-188 10 p.

  Research output: Contribution to journal › Article › peer-review
• 2014

  Artificial Biochemical Networks: Evolving Dynamical Systems to Control Dynamical Systems

  Lones, M. A., Fuente, L. A., Turner, A. P., Caves, L., Stepney, S., Smith, S. L. & Tyrrell, A., Apr 2014, In: IEEE Transactions on Evolutionary Computation. 18, 2, p. 145-166 22 p., 6423886.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Conserved two-step regulatory mechanism of human epithelial differentiation

  Rane, J. K., Droop, A. P., Pellacani, D., Polson, E. S., Simms, M. S., Collins, A. T., Caves, L. S. D. & Maitland, N. J., 11 Feb 2014, In: Stem cell reviews and reports. 2, 2, p. 180-188 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2013

  Adaptive Robotic Gait Control using coupled Artificial Signalling Networks, Hopf Oscillators and Inverse Kinematics

  Fuente, L. A., Lones, M. A., Turner, A. P., Caves, L., Stepney, S. & Tyrrell, A., Jun 2013, p. 1435-1442.

  Research output: Contribution to conference › Paper › peer-review

• Biochemical Connectionism

  Lones, M. A., Turner, A. P., Fuente, L. A., Stepney, S., Caves, L. & Tyrrell, A., Dec 2013, In: Natural Computing. 12, 4, p. 453-472 20 p.

  Research output: Contribution to journal › Article › peer-review

• Computational models of signalling networks for non-linear control

  Fuente, L. A., Lones, M. A., Turner, A. P., Stepney, S., Caves, L. S. & Tyrrell, A. M., May 2013, In: Biosystems. 112, 2, p. 122-130

  Research output: Contribution to journal › Article › peer-review

• On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study

  ElSawy, K. M., Verma, C. S., Joseph, T. L., Lane, D. P., Twarock, R. & Caves, L. S. D., 1 Feb 2013, In: Cell cycle. 12, 3, p. 394-404 11 p.

  Research output: Contribution to journal › Article › peer-review

• The Artificial Epigenetic Network

  Turner, A. P., Lones, M. A., Fuente, L. A., Stepney, S., Caves, L. & Tyrrell, A., Apr 2013, p. 66-72.

  Research output: Contribution to conference › Paper › peer-review

• The incorporation of epigenetics in artificial gene regulatory networks

  Turner, A. P., Lones, M. A., Fuente, L. A., Stepney, S., Caves, L. S. D. & Tyrrell, A. M., May 2013, In: Biosystems. 112, 2, p. 56-62 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2012

  Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development

  ElSawy, K. M., Twarock, R., Lane, D. P., Verma, C. S. & Caves, L. S. D., 10 Jan 2012, In: Journal of chemical theory and computation. 8, 1, p. 314-321 8 p.

  Research output: Contribution to journal › Article › peer-review

• Evolved Artificial Signaling Networks for the Control of a Conservative Complex Dynamical System

  Fuente, L. A., Lones, M. A., Turner, A. P., Stepney, S., Caves, L. & Tyrrell, A., Mar 2012, p. -. 8 p.

  Research output: Contribution to conference › Paper › peer-review

• Peptide Inhibitors of Viral Assembly: A Novel Route to Broad-Spectrum Antivirals

  ElSawy, K. M., Twarock, R., Verma, C. S. & Caves, L. S. D., 26 Mar 2012, In: Journal of chemical information and modeling. 52, 3, p. 770-776 7 p.

  Research output: Contribution to journal › Article › peer-review

• Using Artificial Epigenetic Regulatory Networks To Control Complex Tasks Within Chaotic Systems

  Turner, A. P., Lones, M. A., Fuente, L. A., Stepney, S., Caves, L. & Tyrrell, A., Mar 2012, p. -. 8 p.

  Research output: Contribution to conference › Paper › peer-review

• 2011

  Controlling Legged Robots with Coupled Artificial Biochemical Networks

  Lones, M. A., Tyrrell, A. M., Stepney, S. & Caves, L. S. D., Aug 2011, p. 465-472.

  Research output: Contribution to conference › Paper › peer-review

• On the Origin of Order in the Genome Organization of ssRNA Viruses

  ElSawy, K. M., Caves, L. S. D. & Twarock, R., 17 Aug 2011, In: Biophysical Journal. 101, 4, p. 774-780 7 p.

  Research output: Contribution to journal › Article › peer-review
• 2010

  Controlling Complex Dynamics with Artificial Biochemical Networks

  Lones, M. A., Tyrrell, A. M., Stepney, S. & Caves, L. S. D., 2010, p. 159-170.

  Research output: Contribution to conference › Paper › peer-review

• Controlling Complex Dynamics with Artificial Biochemical Networks

  Lones, M. A., Tyrrell, A. M., Stepney, S. & Caves, L. S., Apr 2010, In: Lecture Notes in Computer Science. 6021, p. 159-170 12 p.

  Research output: Contribution to journal › Article › peer-review

• The Impact of Viral RNA on the Association Rates of Capsid Protein Assembly: Bacteriophage MS2 as a Case Study

  ElSawy, K. M., Caves, L. S. D. & Twarock, R., 23 Jul 2010, In: Journal of Molecular Biology. 400, 4, p. 935-947 13 p.

  Research output: Contribution to journal › Article › peer-review
• 2009

  Cotranslational Protein Folding with L-systems

  Danks, G. B., Stepney, S., Caves, L. S. D., Kampis, G., Karsai, I. & Szathmáry, E., 2009, p. 289-296.

  Research output: Contribution to conference › Paper

• RBN-World: A Sub-symbolic Artificial Chemistry

  Faulconbridge, A., Stepney, S., Miller, J. F. & Caves, L. S. D., 2009, p. 377-384.

  Research output: Contribution to conference › Paper
• 2008

  Polyomaviridae assembly polymorphism from an energy landscape perspective

  ElSawy, K. M., Caves, L. S. D. & Twarock, R., 1 Apr 2008, In: Computational and Mathematical Methods in Medicine. 9, 3-4, p. 245-256 12 p.

  Research output: Contribution to journal › Article › peer-review

• Protein folding with stochastic L-Systems

  Danks, G., Stepney, S. & Caves, L., 2008, p. 150-157.

  Research output: Contribution to conference › Paper
• 2007

  Folding protein-like structures with open L-systems

  Danks, G. B., Stepney, S. & Caves, L. S. D., 2007, Advances in Artificial Life, Proceedings. Costa, FAE., Rocha, LM., Costa, E., Harvey, I. & Coutinho, A. (eds.). BERLIN: Springer, p. 1100-1109 10 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Folding Protein-Like Structures with Open L-Systems

  Danks, G. B., Stepney, S. & Caves, L. S. D., 2007, p. 1100-1109.

  Research output: Contribution to conference › Paper

• Multivariate analysis of conserved sequence-structure relationships in kinesins: Coupling of the active site and a tubulin-binding sub-domain

  Grant, B. J., McCammon, J. A., Caves, L. S. D. & Cross, R. A., 18 May 2007, In: Journal of Molecular Biology. 368, 5, p. 1231-1248 18 p.

  Research output: Contribution to journal › Article › peer-review
• 2006

  Bio3d: an R package for the comparative analysis of protein structures

  Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A. & Caves, L. S. D., 1 Nov 2006, In: Bioinformatics. 22, 21, p. 2695-2696 2 p.

  Research output: Contribution to journal › Article › peer-review
• 2005

  Mutation in myosin heavy chain 6 causes atrial septal defect

  Ching, Y. H., Ghosh, T. K., Cross, S. J., Packham, E. A., Honeyman, L., Loughna, S., Robinson, T. E., Dearlove, A. M., Ribas, G., Bonser, A. J., Thomas, N. R., Scotter, A. J., Caves, L. S. D., Tyrrell, G. P., Newbury-Ecob, R. A., Munnich, A., Bonnet, D. & Brook, J. D., Apr 2005, In: Nature genetics. 37, 4, p. 423-428 6 p.

  Research output: Contribution to journal › Article › peer-review

• The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

  Elsawy, K. M., Hodgson, M. K. & Caves, L. S. D., Oct 2005, In: Nucleic Acids Research. 33, 18, p. 5749-5762 14 p.

  Research output: Contribution to journal › Article › peer-review
• 2004

  Acquiring a Debt Worth Repaying: why Evolutionary Computation should gain yet further inspiration from Biology

  Caves, L., Clark, J. A. & Stepney, S., 2004.

  Research output: Contribution to conference › Paper
• 2003

  Molecular evolutionary convergence of the flight muscle protein arthrin in diptera and hemiptera

  Schmitz, S., Schankin, C. J., Prinz, H., Curwen, R. S., Ashton, P. D., Caves, L. S. D., Fink, R. H. A., Sparrow, J. C., Mayhew, P. J. & Veigel, C., Dec 2003, In: Molecular Biology and Evolution. 20, 12, p. 2019-2033 15 p.

  Research output: Contribution to journal › Article › peer-review
• 2002

  Congruent qualitative behavior of complete and reconstructed phase space trajectories from biomolecular dynamics simulation

  Caves, L. S. D. & Verma, C. S., 1 Apr 2002, In: Proteins - Structure Function and Genetics. 47, 1, p. 25-30 5 p.

  Research output: Contribution to journal › Article › peer-review

• Dynamics of Rnase Sa: A simulation perspective complementary to NMR/X-ray

  Dvorsky, R., Hornak, V., Sevcik, J., Tyrrell, G. P., Caves, L. S. D. & Verma, C. S., 13 Jun 2002, In: Journal of Physical Chemistry B. 106, 23, p. 6038-6048 11 p.

  Research output: Contribution to journal › Article › peer-review

• Inherent flexibility of calmodulin domains: A normal-mode analysis study

  Barton, N. P., Caves, L. S. D. & Verma, C. S., 24 Oct 2002, In: Journal of Physical Chemistry B. 106, 42, p. 11036-11040 5 p.

  Research output: Contribution to journal › Article › peer-review
• 2001

  Understanding the mechanism of ice binding by type III antifreeze proteins

  Antson, A. A., Smith, D. J., Roper, D. I., Lewis, S., Caves, L. S. D., Verma, C. S., Buckley, S. L., Lillford, P. J. & Hubbard, R. E., 26 Jan 2001, In: Journal of Molecular Biology. 305, 4, p. 875-889 15 p.

  Research output: Contribution to journal › Article › peer-review
• 2000

  MBO(N)D: A multibody method for long-time molecular dynamics simulations

  Chun, H. M., Padilla, C. E., Chin, D. N., Watanabe, M., Karlov, V. I., Alper, H. E., Soosaar, K., Blair, K. B., Becker, O. M., Caves, L. S. D., Nagle, R., Haney, D. N. & Farmer, B. L., Feb 2000, In: Journal of computational chemistry. 21, 3, p. 159-184 26 p.

  Research output: Contribution to journal › Literature review › peer-review

• Temperature effects on protein motions: A molecular dynamics study of RNase-Sa

  Dvorsky, R., Sevcik, J., Caves, L. S. D., Hubbard, R. E. & Verma, C. S., 9 Nov 2000, In: Journal of Physical Chemistry B. 104, 44, p. 10387-10397 11 p.

  Research output: Contribution to journal › Article › peer-review
• 1999

  Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric

  Jaaskelainen, S., Verma, C. S., Hubbard, R. E. & Caves, L. S. D., Feb 1999, In: THEORETICAL CHEMISTRY ACCOUNTS. 101, 1-3, p. 175-179 5 p.

  Research output: Contribution to journal › Article › peer-review

• Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol

  English, A. C., Done, S. H., Caves, L. S. D., Groom, C. R. & Hubbard, R. E., 1 Dec 1999, In: Proteins - Structure Function and Genetics. 37, 4, p. 628-640 13 p.

  Research output: Contribution to journal › Article › peer-review

• Structural consequences of the B5 histidine -> tyrosine mutation in human insulin characterized by x-ray crystallography and conformational analysis

  Tang, L., Whittingham, J. L., Verma, C. S., Caves, L. S. D. & Dodson, G. G., 14 Sept 1999, In: Biochemistry. 38, 37, p. 12041-12051 11 p.

  Research output: Contribution to journal › Article › peer-review

• 1998

  Combined biophysical and biochemical information can determine the architecture of transmembrane domains of helical, integral membrane proteins

  Herzyk, P., Afshar, M., Caves, L. S. D. & Hubbard, R. E., 1998, In: JOURNAL OF MOLECULAR GRAPHICS. 16, 4-6, p. 288-288 1 p.

  Research output: Contribution to journal › Article › peer-review

• Conformational change in the activation of lipase: An analysis in terms of low-frequency normal modes

  Jaaskelainen, S., Verma, C. S., Hubbard, R. E., Linko, P. & Caves, L. S. D., Jun 1998, In: Protein Science. 7, 6, p. 1359-1367 9 p.

  Research output: Contribution to journal › Article › peer-review

• Efficiently simulating large molecules using multibody dynamics

  Chin, D. N., Chun, H. M. & Caves, L., 1998, In: JOURNAL OF MOLECULAR GRAPHICS. 16, 4-6, p. 291-291 1 p.

  Research output: Contribution to journal › Article › peer-review

• Modelling molecular motor mechanics: Structural compliance in myosin S1

  Tyrrell, G. P. & Caves, L. S. D., 1998, In: JOURNAL OF MOLECULAR GRAPHICS. 16, 4-6, p. 290-290 1 p.

  Research output: Contribution to journal › Article › peer-review

• 1997

  Domain motions in dihydrofolate reductase: A molecular dynamics study

  Verma, C. S., Caves, L. S. D., Hubbard, R. E. & Roberts, G. C. K., 7 Mar 1997, In: Journal of Molecular Biology. 266, 4, p. 776-796 21 p.

  Research output: Contribution to journal › Literature review › peer-review

• 1996

  Calculation of the reaction pathway for the aromatic ring flip in methotrexate complexed to dihydrofolate reductase

  Verma, C. S., Fischer, S., Caves, L. S. D., Roberts, G. C. K. & Hubbard, R. E., 15 Feb 1996, In: Journal of Physical Chemistry. 100, 7, p. 2510-2518 9 p.

  Research output: Contribution to journal › Article › peer-review

• Demonstration that 1-trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane (E-64) is one of the most effective low M(r) inhibitors of trypsin-catalysed hydrolysis. Characterization by kinetic analysis and by energy minimization and molecular dynamics simulation of the E-64-beta-trypsin complex

  Sreedharan, S. K., Verma, C., Caves, L. S. D., Brocklehurst, S. M., Gharbia, S. E., Shah, H. N. & Brocklehurst, K., 15 Jun 1996, In: Biochemical journal. 316, p. 777-786 10 p.

  Research output: Contribution to journal › Article › peer-review

• 1994

  INVESTIGATING THE HIGH-AFFINITY AND LOW SEQUENCE SPECIFICITY OF CALMODULIN-BINDING TO ITS TARGETS

  AFSHAR, M., CAVES, L. S. D., GUIMARD, L., HUBBARD, R. E., CALAS, B., GRASSY, G. & HAIECH, J., 16 Dec 1994, In: Journal of Molecular Biology. 244, 5, p. 554-571 18 p.

  Research output: Contribution to journal › Article › peer-review