Richard M Jackson

Richard M Jackson

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Richard M Jackson

Richard M Jackson

Publications by authors named "Richard M Jackson"

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Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities.

J Phys Chem B 2012 Sep 27;116(35):10856-69. Epub 2012 Aug 27.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.

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http://dx.doi.org/10.1021/jp209041xDOI Listing
September 2012

Hierarchical bayesian modeling of pharmacophores in bioinformatics.

Biometrics 2011 Jun 9;67(2):611-9. Epub 2010 Jul 9.

Department of Statistics, The University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1111/j.1541-0420.2010.01460.xDOI Listing
June 2011

Correction to "Machine learning-based method to improve docking scoring functions and its application to drug repurposing".

J Chem Inf Model 2011 May 28;51(5):1195-7. Epub 2011 Apr 28.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom.

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http://dx.doi.org/10.1021/ci2001346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186856PMC
May 2011

ReverseScreen3D: a structure-based ligand matching method to identify protein targets.

J Chem Inf Model 2011 Mar 28;51(3):624-34. Epub 2011 Feb 28.

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.

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http://dx.doi.org/10.1021/ci1003174DOI Listing
March 2011

A machine learning-based method to improve docking scoring functions and its application to drug repurposing.

J Chem Inf Model 2011 Feb 3;51(2):408-19. Epub 2011 Feb 3.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.

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http://dx.doi.org/10.1021/ci100369fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076728PMC
February 2011

The Mycobacterium tuberculosis drugome and its polypharmacological implications.

PLoS Comput Biol 2010 Nov 4;6(11):e1000976. Epub 2010 Nov 4.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.

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http://dx.plos.org/10.1371/journal.pcbi.1000976
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http://dx.doi.org/10.1371/journal.pcbi.1000976DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973814PMC
November 2010

Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods.

J Chem Inf Model 2010 Oct;50(10):1806-20

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.

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http://pubs.acs.org/doi/abs/10.1021/ci100250z
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http://dx.doi.org/10.1021/ci100250zDOI Listing
October 2010

Homology-modelling protein-ligand interactions: allowing for ligand-induced conformational change.

J Mol Biol 2010 Jun 29;399(4):645-61. Epub 2010 Apr 29.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1016/j.jmb.2010.04.047DOI Listing
June 2010

InCa-SiteFinder: a method for structure-based prediction of inositol and carbohydrate binding sites on proteins.

J Mol Graph Model 2009 Oct 27;28(3):297-303. Epub 2009 Aug 27.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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http://dx.doi.org/10.1016/j.jmgm.2009.08.009DOI Listing
October 2009

LigMatch: a multiple structure-based ligand matching method for 3D virtual screening.

J Chem Inf Model 2009 Sep;49(9):2056-66

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.

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http://pubs.acs.org/doi/abs/10.1021/ci900204y
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http://dx.doi.org/10.1021/ci900204yDOI Listing
September 2009

Predicting druggable binding sites at the protein-protein interface.

Drug Discov Today 2009 Feb 16;14(3-4):155-61. Epub 2008 Dec 16.

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1016/j.drudis.2008.10.009DOI Listing
February 2009

Binding site similarity analysis for the functional classification of the protein kinase family.

J Chem Inf Model 2009 Feb;49(2):318-29

Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1021/ci800289yDOI Listing
February 2009

Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity.

J Chem Inf Model 2008 Oct 4;48(10):1990-8. Epub 2008 Sep 4.

Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, Dortmund, Germany.

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http://dx.doi.org/10.1021/ci800125kDOI Listing
October 2008

An evaluation of automated homology modelling methods at low target template sequence similarity.

Bioinformatics 2007 Aug 17;23(15):1901-8. Epub 2007 May 17.

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btm262DOI Listing
August 2007

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

BMC Genomics 2007 Jun 27;8:194. Epub 2007 Jun 27.

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.

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http://dx.doi.org/10.1186/1471-2164-8-194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925091PMC
June 2007

Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking.

Bioinformatics 2007 Mar 18;23(5):573-81. Epub 2007 Jan 18.

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.

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http://dx.doi.org/10.1093/bioinformatics/btl661DOI Listing
March 2007

Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening.

Curr Protein Pept Sci 2006 Oct;7(5):395-406

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.

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October 2006

Structure-based pharmacophore design and virtual screening for novel angiotensin converting enzyme 2 inhibitors.

J Chem Inf Model 2006 Mar-Apr;46(2):708-16

Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1021/ci0503614DOI Listing
September 2006

A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships.

J Chem Inf Model 2006 Mar-Apr;46(2):736-42

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1021/ci050359cDOI Listing
September 2006

Delineation and modelling of a nucleolar retention signal in the coronavirus nucleocapsid protein.

Traffic 2006 Jul 25;7(7):833-48. Epub 2006 May 25.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK.

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http://dx.doi.org/10.1111/j.1600-0854.2006.00424.xDOI Listing
July 2006

Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces.

Bioinformatics 2006 Jun 7;22(11):1335-42. Epub 2006 Mar 7.

Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btl079DOI Listing
June 2006

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.

J Mol Biol 2006 Feb 1;355(5):1112-24. Epub 2005 Dec 1.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1016/j.jmb.2005.11.044DOI Listing
February 2006

SitesBase: a database for structure-based protein-ligand binding site comparisons.

Nucleic Acids Res 2006 Jan;34(Database issue):D231-4

Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1093/nar/gkj062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347425PMC
January 2006

Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.

Bioinformatics 2005 Aug 16;21(16):3360-8. Epub 2005 Jun 16.

Grup de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti522DOI Listing
August 2005

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

Bioinformatics 2005 May 8;21(9):1908-16. Epub 2005 Feb 8.

School of Biochemistry and Microbiology, University of Leeds, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti315DOI Listing
May 2005

Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching.

Proteins 2004 Aug;56(2):250-60

Department of Biochemistry & Molecular Biology, University College London, Gower Street, London, England.

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http://dx.doi.org/10.1002/prot.20123DOI Listing
August 2004

Angiotensin-converting enzyme-2 (ACE2): comparative modeling of the active site, specificity requirements, and chloride dependence.

Biochemistry 2003 Nov;42(45):13185-92

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.

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http://pubs.acs.org/doi/abs/10.1021/bi035268s
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http://dx.doi.org/10.1021/bi035268sDOI Listing
November 2003

Ligand binding: functional site location, similarity and docking.

Curr Opin Struct Biol 2003 Jun;13(3):389-95

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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June 2003

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.

J Comput Aided Mol Des 2002 Jan;16(1):43-57

Department of Biochemistry and Molecular Biology, University College, London, UK.

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January 2002