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Year Number of Results
2004 1
2005 1
2006 1
2007 1
2009 1
2010 3
2011 4
2012 7
2013 1
2014 4
2015 3
2018 1
2020 1
2021 0
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29 results
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Page 1
Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer.
Hall BA, Fisher J. Hall BA, et al. Curr Protoc Bioinformatics. 2020 Mar;69(1):e95. doi: 10.1002/cpbi.95. Curr Protoc Bioinformatics. 2020. PMID: 32078258
After the appropriate functions for each variable are defined, the user has access to three analysis engines to test the model. In addition to standard simulation tools, BMA includes an interface to the stability-testing algorithm and to a graphical Linear Temporal Logi
After the appropriate functions for each variable are defined, the user has access to three analysis engines to test the model. In addition …
A toolbox for discrete modelling of cell signalling dynamics.
Paterson YZ, Shorthouse D, Pleijzier MW, Piterman N, Bendtsen C, Hall BA, Fisher J. Paterson YZ, et al. Among authors: hall ba. Integr Biol (Camb). 2018 Jun 18;10(6):370-382. doi: 10.1039/c8ib00026c. Integr Biol (Camb). 2018. PMID: 29855020
In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. ...This new library …
In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards syst …
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.
Wright DW, Hall BA, Kenway OA, Jha S, Coveney PV. Wright DW, et al. Among authors: hall ba. J Chem Theory Comput. 2014 Mar 11;10(3):1228-1241. doi: 10.1021/ct4007037. Epub 2014 Jan 27. J Chem Theory Comput. 2014. PMID: 24683369 Free PMC article.
In order to realize the potential of such approaches to predict new results, not merely to explain previous experimental findings, it is necessary that the methods used are reliable and accurate, and that their limitations are thoroughly understood. However, the computational
In order to realize the potential of such approaches to predict new results, not merely to explain previous experimental findings, it is nec …
Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis.
Hall BA, Jackson E, Hajnal A, Fisher J. Hall BA, et al. J R Soc Interface. 2014 Sep 6;11(98):20140245. doi: 10.1098/rsif.2014.0245. J R Soc Interface. 2014. PMID: 24966232 Free PMC article.
Modelling cell fate determination in vulval development using state-based models, coupled with formal analysis techniques, has been established as a powerful approach in predicting the outcome of combinations of mutations. However, computing the outcomes of complex and hig …
Modelling cell fate determination in vulval development using state-based models, coupled with formal analysis techniques, has been establis …
Accommodation of a central arginine in a transmembrane peptide by changing the placement of anchor residues.
Vostrikov VV, Hall BA, Sansom MS, Koeppe RE 2nd. Vostrikov VV, et al. Among authors: hall ba. J Phys Chem B. 2012 Nov 1;116(43):12980-90. doi: 10.1021/jp308182b. Epub 2012 Oct 17. J Phys Chem B. 2012. PMID: 23030363 Free PMC article.
The locations and orientations of the peptides with respect to lipid bilayer membranes of differing thickness were investigated by means of solid-state (2)H NMR spectroscopy, using labeled alanines, and coarse-grained molecular dynamics simulations. Interestingly, relative …
The locations and orientations of the peptides with respect to lipid bilayer membranes of differing thickness were investigated by means of …
Characterization of protein conformational states by normal-mode frequencies.
Hall BA, Kaye SL, Pang A, Perera R, Biggin PC. Hall BA, et al. J Am Chem Soc. 2007 Sep 19;129(37):11394-401. doi: 10.1021/ja071797y. Epub 2007 Aug 23. J Am Chem Soc. 2007. PMID: 17715919
Defining conformational states, however, remains a difficult and increasingly common problem, with many existing methods based on arbitrary or potentially unrepresentative measures. Furthermore, the expanding length of molecular dynamics simulations and direct observation …
Defining conformational states, however, remains a difficult and increasingly common problem, with many existing methods based on arbitrary …
Drug target optimization in chronic myeloid leukemia using innovative computational platform.
Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi M, Koschmieder S, Gottgens B, Fisher J. Chuang R, et al. Among authors: hall ba. Sci Rep. 2015 Feb 3;5:8190. doi: 10.1038/srep08190. Sci Rep. 2015. PMID: 25644994 Free PMC article.
To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that regulates the disease. The BioModelAnalyzer (BMA) is a user-friendly computational tool that allows us to do exactly that. We used BMA t …
To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that reg …
Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices.
Hall BA, Halim KB, Buyan A, Emmanouil B, Sansom MS. Hall BA, et al. J Chem Theory Comput. 2014 May 13;10(5):2165-75. doi: 10.1021/ct500003g. J Chem Theory Comput. 2014. PMID: 26580541 Free PMC article.
These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. ...In a second application, we use CGMD …
These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analy …
Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling.
Hall BA, Piterman N, Hajnal A, Fisher J. Hall BA, et al. Biophys J. 2015 Jul 21;109(2):428-38. doi: 10.1016/j.bpj.2015.06.007. Biophys J. 2015. PMID: 26200879 Free PMC article.
Stem cells respond to temporally and spatially regulated signals by switching from mitotic proliferation to asymmetric cell division and differentiation. Executable computer models of signaling pathways can accurately reproduce a wide range of biological phenomena by reduc …
Stem cells respond to temporally and spatially regulated signals by switching from mitotic proliferation to asymmetric cell division and dif …
Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling.
Hall BA, Armitage JP, Sansom MS. Hall BA, et al. PLoS Comput Biol. 2011 Oct;7(10):e1002204. doi: 10.1371/journal.pcbi.1002204. Epub 2011 Oct 20. PLoS Comput Biol. 2011. PMID: 22028633 Free PMC article.
We focus on the position (shift) and orientation (tilt, rotation) of TM2 relative to the bilayer and how these are perturbed in mutants relative to the wildtype. The simulations reveal a clear correlation between small (ca. 1.5 A) shift in position of TM2 along the bilayer …
We focus on the position (shift) and orientation (tilt, rotation) of TM2 relative to the bilayer and how these are perturbed in mutants rela …
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