Publications by authors named "Tom L Blundell"

100Publications

Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM.

Prog Biophys Mol Biol 2020 Dec 4. Epub 2020 Dec 4.

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK. Electronic address:

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December 2020

Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance.

Front Genet 2020 4;11:965. Epub 2020 Sep 4.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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September 2020

Interdisciplinary research in physics, chemistry and biology is central to understanding biological processes.

Authors:
Tom L Blundell

Prog Biophys Mol Biol 2020 10;156:1-2

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK. Electronic address:

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October 2020

Systematic Investigation of the Data Set Dependency of Protein Stability Predictors.

J Chem Inf Model 2020 Oct 24;60(10):4772-4784. Epub 2020 Aug 24.

DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, Denmark.

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October 2020

Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions.

Prog Biophys Mol Biol 2020 10 3;156:34-42. Epub 2020 Jul 3.

Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Prof C.R. Rao Road, Hyderabad, India. Electronic address:

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October 2020

Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining.

Essays Biochem 2020 10;64(5):791-806

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21GA, Cambridgeshire, U.K.

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October 2020

Common mechanism of thermostability in small α- and β-proteins studied by molecular dynamics.

Proteins 2020 09 19;88(9):1233-1250. Epub 2020 May 19.

DTU Chemistry, Technical University of Denmark, Lyngby, Denmark.

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September 2020

Fragment-Based Design of InhA Inhibitors.

J Med Chem 2020 05 15;63(9):4749-4761. Epub 2020 Apr 15.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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May 2020

Editorial overview: Macromolecular assemblies.

Curr Opin Struct Biol 2020 04 9;61:vi-viii. Epub 2020 Mar 9.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom. Electronic address:

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April 2020

A platform for target prediction of phenotypic screening hit molecules.

J Mol Graph Model 2020 03 24;95:107485. Epub 2019 Oct 24.

Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH, United Kingdom. Electronic address:

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March 2020

Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH).

Bioorg Med Chem Lett 2020 01 9;30(2):126792. Epub 2019 Nov 9.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom. Electronic address:

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January 2020

Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining.

Curr Opin Struct Biol 2020 04 14;61:9-16. Epub 2019 Nov 14.

Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, United Kingdom. Electronic address:

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April 2020

Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning.

Protein Sci 2020 01 25;29(1):247-257. Epub 2019 Nov 25.

Department of Biochemistry, University of Cambridge, Cambridge, UK.

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January 2020

ProCarbDB: a database of carbohydrate-binding proteins.

Nucleic Acids Res 2020 01;48(D1):D368-D375

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.

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January 2020

SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange.

Prog Biophys Mol Biol 2019 10 27;147:92-102. Epub 2019 Sep 27.

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA.

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October 2019

Editorial overview: Theory and simulation: demystifying GPCRs - structure, function and drug design.

Curr Opin Struct Biol 2019 04;55:vi-viii

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. Electronic address:

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April 2019

Multicomponent assemblies in DNA-double-strand break repair by NHEJ.

Curr Opin Struct Biol 2019 04 21;55:154-160. Epub 2019 May 21.

Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK. Electronic address:

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April 2019

Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH.

Eur J Med Chem 2019 Jul 15;174:309-329. Epub 2019 Apr 15.

MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa. Electronic address:

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July 2019

Understanding the structure and role of DNA-PK in NHEJ: How X-ray diffraction and cryo-EM contribute in complementary ways.

Prog Biophys Mol Biol 2019 10 20;147:26-32. Epub 2019 Apr 20.

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK. Electronic address:

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October 2019

Editorial.

Prog Biophys Mol Biol 2019 01;141:1-2

Institute for Experimental Cardiovascular Medicine, Faculty of Medicine, University of Freiburg, Elsasser Str 2Q, 90110, Freiburg, Germany. Electronic address:

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January 2019

The deubiquitylating enzyme UCHL3 regulates Ku80 retention at sites of DNA damage.

Sci Rep 2018 12 17;8(1):17891. Epub 2018 Dec 17.

Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, United Kingdom.

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December 2018

Progress in biophysics and molecular biology: A brief history of the journal.

Prog Biophys Mol Biol 2018 12;140:1-4

Institute for Experimental Cardiovascular Medicine, Faculty of Medicine, University of Freiburg, Elsasser Str 2Q, 90110, Freiburg, Germany. Electronic address:

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December 2018

Arginine-deprivation-induced oxidative damage sterilizes .

Proc Natl Acad Sci U S A 2018 09 24;115(39):9779-9784. Epub 2018 Aug 24.

Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461;

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September 2018

Dissection of DNA double-strand-break repair using novel single-molecule forceps.

Nat Struct Mol Biol 2018 06 21;25(6):482-487. Epub 2018 May 21.

Institut Jacques Monod, Université Paris Diderot, CNRS, UMR 7592, Paris, France.

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June 2018

Fragment-Based Approach to Targeting Inosine-5'-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis.

J Med Chem 2018 04 23;61(7):2806-2822. Epub 2018 Mar 23.

Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.

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April 2018

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species.

Database (Oxford) 2017 01;2017

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.

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January 2017

Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry.

Authors:
Tom L Blundell

IUCrJ 2017 Jul 29;4(Pt 4):308-321. Epub 2017 Jun 29.

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England.

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July 2017

Decoding the similarities and differences among mycobacterial species.

PLoS Negl Trop Dis 2017 Aug 30;11(8):e0005883. Epub 2017 Aug 30.

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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August 2017

Correction for Arora et al., "Respiratory Flexibility in Response to Inhibition of Cytochrome Oxidase in ".

Antimicrob Agents Chemother 2017 09 24;61(9). Epub 2017 Aug 24.

Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA.

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September 2017

Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.

J Mol Biol 2017 08 23;429(17):2677-2693. Epub 2017 Jun 23.

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK. Electronic address:

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August 2017

SDM: a server for predicting effects of mutations on protein stability.

Nucleic Acids Res 2017 07;45(W1):W229-W235

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.

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July 2017

Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry.

Angew Chem Int Ed Engl 2017 06 31;56(26):7488-7491. Epub 2017 May 31.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

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June 2017

XSuLT: a web server for structural annotation and representation of sequence-structure alignments.

Nucleic Acids Res 2017 07;45(W1):W381-W387

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.

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July 2017

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.

Science 2017 02 2;355(6324):520-524. Epub 2017 Feb 2.

Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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February 2017

Structure-guided, target-based drug discovery - exploiting genome information from HIV to mycobacterial infections.

Postepy Biochem 2016;62(3):262-272

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.

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December 2017

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.

J Mol Biol 2017 02 10;429(3):365-371. Epub 2016 Dec 10.

Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address:

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February 2017

Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health.

Prog Biophys Mol Biol 2017 09 29;128:3-13. Epub 2016 Nov 29.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Department of Biochemistry, University of Melbourne, Melbourne, 3052, Australia. Electronic address:

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September 2017

Targeting tuberculosis using structure-guided fragment-based drug design.

Drug Discov Today 2017 03 11;22(3):546-554. Epub 2016 Oct 11.

Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK. Electronic address:

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March 2017

Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency.

J Biol Chem 2016 Nov 4;291(47):24377-24389. Epub 2016 Oct 4.

From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and

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November 2016

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis.

ACS Infect Dis 2017 01 8;3(1):5-17. Epub 2016 Sep 8.

MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town , Anzio Road, Observatory 7925, South Africa.

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January 2017

ATP half-sites in RadA and RAD51 recombinases bind nucleotides.

FEBS Open Bio 2016 05 6;6(5):372-85. Epub 2016 Apr 6.

Department of Biochemistry University of Cambridge UK.

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May 2016

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.

Sci Rep 2016 07 7;6:29575. Epub 2016 Jul 7.

Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.

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July 2016

Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

J Med Chem 2016 05 11;59(9):4314-25. Epub 2016 Apr 11.

Department of Biochemistry, University of Cambridge , Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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May 2016

Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction.

FEBS Lett 2016 04 6;590(8):1094-102. Epub 2016 Apr 6.

Department of Biochemistry, University of Cambridge, Cambridge, UK.

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April 2016

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.

Sci Rep 2016 Jan 22;6:19848. Epub 2016 Jan 22.

Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.

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January 2016

Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.

Mol Cell 2016 Feb 14;61(3):434-448. Epub 2016 Jan 14.

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK. Electronic address:

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February 2016

Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein.

Open Biol 2015 Dec;5(12):150174

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

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December 2015

Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors.

Prog Biophys Mol Biol 2015 Sep 5;118(3):103-11. Epub 2015 May 5.

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address:

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September 2015

Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma.

Cancer Discov 2015 Jul 14;5(7):723-9. Epub 2015 Apr 14.

Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom.

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July 2015

pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures.

J Med Chem 2015 May 22;58(9):4066-72. Epub 2015 Apr 22.

†Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Sanger Building, Cambridge, Cambridgshire CB2 1GA, U.K.

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May 2015

CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.

Database (Oxford) 2015 31;2015. Epub 2015 Mar 31.

Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India.

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September 2015

Phosphopeptide interactions with BRCA1 BRCT domains: More than just a motif.

Prog Biophys Mol Biol 2015 Mar 17;117(2-3):143-148. Epub 2015 Feb 17.

Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, Cambridge, United Kingdom.

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March 2015

Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations.

JIMD Rep 2015 15;24:3-11. Epub 2015 Feb 15.

Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospital Trust, Duncan Building, Liverpool, L7 8XP, UK.

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September 2015

Flexibility and small pockets at protein-protein interfaces: New insights into druggability.

Prog Biophys Mol Biol 2015 Oct 7;119(1):2-9. Epub 2015 Feb 7.

Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address:

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October 2015