Brian Marsden

Principal Investigator

University of Oxford

SGC Oxford’s Research Informatics group has a number of distinct roles. (1) Informatics; developing novel methods for data capture, mining and visualisation using LIMS (Laboratory Information Management Systems). (2) Bioinformatics & computational chemistry; supporting the SGC structural biology and chemical probes pipeline. (3) Structural Biology data annotation and dissemination. (4) Providing a full range of IT services and support to SGC Oxford scientists.

Research Areas

The Research Informatics group is a joint collaboration between the SGC and Kennedy Institute. A primary interest of the group is the development of novel ways to make structural and chemical biology data accessible to non-experts. By using modern technologies to provide interactive and immersive visualisations we make it easier for the SGC’s output to be interpreted by scientists who are not structural or chemical biologists. Our second primary interest is in the continuing development of integrated LIMS in order to ensure that the SGC’s work is capture and easily mined, thereby enhancing our efficiency and productivity. As part of this work we also maintain the SGC target list using bioinformatics tools and ensure that data is shared appropriately between SGC sites and the scientific community at large.

Group Members

  • David Damerell
  • Leonidas Koukouflis
  • Uka Osim
  • Christopher Sluman

Publications

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
Bradley, AR; Wall, ID; von Delft, F; Green, DV; Deane, CM; Marsden, BD;
Journal of Computer-Aided Molecular Design. 2015 29:963-973. doi:
PMID: 26387008

OOMMPPAA: a tool to aid directed synthesis by the combined analysis of activity and structural data.
Bradley, AR; Wall, ID; Green, DV; Deane, CM; Marsden, BD;
Journal of Chemical Information and Modeling. 2014 54:2636-2646. doi:
PMID: 25244105

A new method for publishing three-dimensional content
Raush, E; Totrov, M; Marsden, BD; Abagyan, R;
PLoS One. 2009 4:-. doi: 10.1371/journal.pone.0007394
PMID: 19841676

SGC--structural biology and human health: a new approach to publishing structural biology results.
Lee, WH; Atienza-Herrero, J; Abagyan, R; Marsden, BD;
PLoS One. 2009 4:e7675-. doi: 10.1371/journal.pone.0007675
PMID: 19847312

Doing more than just the structure-structural genomics in kinase drug discovery.
Marsden, BD; Knapp, S;
Current Opinion in Chemical Biology. 2008 12:40-45. doi: 10.1016/j.cbpa.2008.01.042
PMID: 18267130

Disseminating structural genomics data to the public: from a data dump to an animated story
Abagyan, R; Lee, WH; Raush, E; Budagyan, L; Totrov, M; Sundstrom, M; Marsden, BD;
Trends in Biochemical Sciences. 2006 31:76-78. doi: 10.1016/j.tibs.2005.12.006
PMID: 16406633

2017

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Pearce, NM; Krojer, T; Bradley, AR; Collins, P; Nowak, RP; Talon, R; Marsden, BD; Kelm, S; Shi, J; Deane, CM; von Delft, F;
Nature Communications. 2017 8:15123-. doi: 10.1038/ncomms15123
PMID: 28436492

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.
Pearce, NM; Bradley, AR; Krojer, T; Marsden, BD; Deane, CM; von Delft, F;
Structural Dynamics. 2017 4:032104-. doi: 10.1063/1.4974176
PMID: 28345007

WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design.
Deane, CM; Wall, ID; Green, DV; Marsden, BD; Bradley, AR;
Acta Crystallographica. Section d, Structural Biology. 2017 73:279-285. doi: 10.1107/S2059798316009529
PMID: 28291763

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.
Krojer, T; Talon, R; Pearce, N; Collins, P; Douangamath, A; Brandao-Neto, J; Dias, A; Marsden, B; von Delft, F;
Acta Crystallographica. Section d, Structural Biology. 2017 73:267-278. doi: 10.1107/S2059798316020234
PMID: 28291762

2016

A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain
Cox, OB; Krojer, T; Collins, P; Monteiro, O; Talon, R; Bradley, A; Fedorov, O; Amin, J; Marsden, BD; Spencer, J; von Delft, F; Brennan, PE;
Chemical Science. 2016 7:2322-2330. doi: 10.1039/c5sc03115j
PMID:

2015

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
Bradley, AR; Wall, ID; von Delft, F; Green, DV; Deane, CM; Marsden, BD;
Journal of Computer-Aided Molecular Design. 2015 29:963-973. doi:
PMID: 26387008

Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.
Wettstein, S; Underhaug, J; Perez, B; Marsden, BD; Yue, WW; Martinez, A; Blau, N;
European Journal of Human Genetics. 2015 23:302-309. doi:
PMID: 24939588

2014

OOMMPPAA: a tool to aid directed synthesis by the combined analysis of activity and structural data.
Bradley, AR; Wall, ID; Green, DV; Deane, CM; Marsden, BD;
Journal of Chemical Information and Modeling. 2014 54:2636-2646. doi:
PMID: 25244105

The Humoral Immune Response to HCV: Understanding is Key to Vaccine Development.
Cashman, SB; Marsden, BD; Dustin, LB;
Frontiers in Immunology. 2014 5:550-. doi:
PMID: 25426115

[1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains.
Fedorov, O; Lingard, H; Wells, C; Monteiro, OP; Picaud, S; Keates, T; Yapp, C; Philpott, M; Martin, SJ; Felletar, I; Marsden, BD; Filippakopoulos, P; Müller, S; Knapp, S; Brennan, PE;
Journal of Medicinal Chemistry. 2014 57:462-476. doi:
PMID: 24313754

2013

Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.
Froese, DS; Forouhar, F; Tran, TH; Vollmar, M; Kim, YS; Lew, S; Neely, H; Seetharaman, J; Shen, Y; Xiao, R; Acton, TB; Everett, JK; Cannone, G; Puranik, S; Savitsky, P; Krojer, T; Pilka, ES; Kiyani, W; Lee, WH; Marsden, BD; von Delft, F; Allerston, CK; Spagnolo, L; Gileadi, O; Montelione, GT; Oppermann, U; Yue, WW; Tong, L;
Structure. 2013 21:1182-1192. doi: 10.1016/j.str.2013.05.001
PMID: 23791943

Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases.
Canning, P; Cooper, CD; Krojer, T; Murray, JW; Pike, AC; Chaikuad, A; Keates, T; Thangaratnarajah, C; Hojzan, V; Ayinampudi, V; Marsden, BD; Gileadi, O; Knapp, S; von Delft, F; Bullock, AN;
Journal of Biological Chemistry. 2013 288:7803-7814. doi: 10.1074/jbc.M112.437996
PMID: 23349464

2012

Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit.
Fish, PV; Filippakopoulos, P; Bish, G; Brennan, PE; Bunnage, ME; Cook, AS; Federov, O; Gerstenberger, BS; Jones, H; Knapp, S; Marsden, B; Nocka, K; Owen, DR; Philpott, M; Picaud, S; Primiano, MJ; Ralph, MJ; Sciammetta, N; Trzupek, JD;
Journal of Medicinal Chemistry. 2012 55:9831-9837. doi:
PMID: 23095041

Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.
Rose, NR; Woon, EC; Tumber, A; Walport, LJ; Chowdhury, R; Li, XS; King, ON; Lejeune, C; Ng, SS; Krojer, T; Chan, MC; Rydzik, AM; Hopkinson, RJ; Che, KH; Daniel, M; Strain-Damerell, C; Gileadi, C; Kochan, G; Leung, IK; Dunford, J; Yeoh, KK; Ratcliffe, PJ; Burgess-Brown, N; von Delft, F; Muller, S; Marsden, B; Brennan, PE; McDonough, MA; Oppermann, U; Klose, RJ; Schofield, CJ; Kawamura, A;
Journal of Medicinal Chemistry. 2012 55:6639-6643. doi: 10.1021/jm300677j
PMID: 22724510

3,5-Dimethylisoxazoles inhibit the bromodomain-histone protein-protein interaction
Hewings, DS; Wang, M; Philpott, M; Fedorov, O; Uttarkar, S; Filippakopoulos, P; Picaud, S; Vuppusetty, C; Marsden, B; Heightman, TD; Knapp, S; Brennan, P; Conway, SJ;
ACS National Meeting Book of Abstracts. 2012 243:-. doi:
PMID:

Developing chemical probes for the BET bromodomains
Hewings, DS; Wang, M; Philpott, M; Fedorov, O; Uttarkar, S; Filippakopoulos, P; Picaud, S; Vuppusetty, C; Marsden, B; Heightman, TD; Knapp, S; Brennan, P; Conway, SJ;
ACS National Meeting Book of Abstracts. 2012 243:-. doi:
PMID:

Linking of 2-oxoglutarate and substrate binding sites enables potent and highly selective inhibition of JmjC histone demethylases.
Woon, EC; Tumber, A; Kawamura, A; Hillringhaus, L; Ge, W; Rose, NR; Ma, JH; Chan, MC; Walport, LJ; Che, KH; Ng, SS; Marsden, BD; Oppermann, U; McDonough, MA; Schofield, CJ;
Angewandte Chemie International Edition. 2012 51:1631-1634. doi: 10.1002/anie.201107833
PMID: 22241642

Click JAHAs: Conformationally restricted ferrocene-based histone deacetylase inhibitors
Spencer, J; Amin, J; Boddiboyena, R; Packham, G; Cavell, BE; Syed Alwi, SS; Paranal, RM; Heightman, TD; Wang, M; Marsden, B; Coxhead, P; Guille, M; Tizzard, GJ; Coles, SJ; Bradner, JE;
MedChemComm. 2012 3:61-64. doi: 10.1039/c1md00203a
PMID:

2011

3,5-dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands.
Hewings, DS; Wang, M; Philpott, M; Fedorov, O; Uttarkar, S; Filippakopoulos, P; Picaud, S; Vuppusetty, C; Marsden, B; Knapp, S; Conway, SJ; Heightman, TD;
Journal of Medicinal Chemistry. 2011 54:6761-6770. doi:
PMID: 21851057

Interactive JIMD articles using the iSee concept: turning a new page on structural biology data
Lee, WH; Yue, WW; Raush, E; Totrov, M; Abagyan, R; Oppermann, U; Marsden, BD;
Journal of Inherited Metabolic Disease. 2011 :1-3. doi: 10.1007/s10545-011-9334-4
PMID: 21509537

INTERACTIVE 3D VISUALISATIONS OF PROTEIN STRUCTURES TO AID THE STUDY OF INBORN ERRORS OF METABOLISM
Lee, WH; Raush, E; Totrov, M; Abagyan, R; Marsden, BD; Oppermann, U; Yue, WW;
Journal of Inherited Metabolic Disease. 2011 34:S240-S240. doi:
PMID:

2010

High-throughput production of human proteins for crystallization: the SGC experience.
Savitsky, P; Bray, J; Cooper, CD; Marsden, BD; Mahajan, P; Burgess-Brown, NA; Gileadi, O;
Journal of Structural Biology. 2010 172:3-13. doi: 10.1016/j.jsb.2010.06.008
PMID: 20541610

Structural comparison of human mammalian ste20-like kinases.
Record, CJ; Chaikuad, A; Rellos, P; Das, S; Pike, AC; Fedorov, O; Marsden, BD; Knapp, S; Lee, WH;
PLoS One. 2010 5:e11905-. doi:
PMID: 20730082

2009

Structure-activity relationships of human AKR-type oxidoreductases involved in bile acid synthesis: AKR1D1 and AKR1C4.
Lee, WH; Lukacik, P; Guo, K; Ugochukwu, E; Kavanagh, KL; Marsden, B; Oppermann, U;
Molecular and Cellular Endocrinology. 2009 301:199-204. doi: 10.1016/j.mce.2008.09.042
PMID: 19013211

The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary.
Bray, JE; Marsden, BD; Oppermann, U;
Chemico-Biological Interactions. 2009 178:99-109. doi: 10.1016/j.cbi.2008.10.058
PMID: 19061874

A new method for publishing three-dimensional content
Raush, E; Totrov, M; Marsden, BD; Abagyan, R;
PLoS One. 2009 4:-. doi: 10.1371/journal.pone.0007394
PMID: 19841676

SGC--structural biology and human health: a new approach to publishing structural biology results.
Lee, WH; Atienza-Herrero, J; Abagyan, R; Marsden, BD;
PLoS One. 2009 4:e7675-. doi: 10.1371/journal.pone.0007675
PMID: 19847312

2008

Doing more than just the structure-structural genomics in kinase drug discovery.
Marsden, BD; Knapp, S;
Current Opinion in Chemical Biology. 2008 12:40-45. doi: 10.1016/j.cbpa.2008.01.042
PMID: 18267130

2007

A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.
Fedorov, O; Marsden, B; Pogacic, V; Rellos, P; Müller, S; Bullock, AN; Schwaller, J; Sundström, M; Knapp, S;
Proceedings of the National Academy of Sciences of USA. 2007 104:20523-20528. doi:
PMID: 18077363

The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.
Gileadi, O; Knapp, S; Lee, WH; Marsden, BD; Müller, S; Niesen, FH; Kavanagh, KL; Ball, LJ; von Delft, F; Doyle, DA; Oppermann, UC; Sundström, M;
Journal of Structural and Functional Genomics. 2007 8:107-119. doi: 10.1007/s10969-007-9027-2
PMID: 17932789

Insights for the development of specific kinase inhibitors by targeted structural genomics.
Fedorov, O; Sundström, M; Marsden, B; Knapp, S;
Drug Discovery Today. 2007 12:365-372. doi:
PMID: 17467572

2006

Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases.
Eswaran, J; von Kries, JP; Marsden, B; Longman, E; Debreczeni, JE; Ugochukwu, E; Turnbull, A; Lee, WH; Knapp, S; Barr, AJ;
Biochemical Journal. 2006 395:483-491. doi: 10.1042/BJ20051931
PMID: 16441242

Gas phase characterization of the noncovalent quaternary structure of cholera toxin and the cholera toxin B subunit pentamer
Williams, JP; Smith, DC; Green, BN; Marsden, BD; Jennings, KR; Roberts, LM; Scrivens, JH;
Biophysical Journal. 2006 90:3246-3254. doi: 10.1529/biophysj.105.076455
PMID: 16461395

Disseminating structural genomics data to the public: from a data dump to an animated story
Abagyan, R; Lee, WH; Raush, E; Budagyan, L; Totrov, M; Sundstrom, M; Marsden, BD;
Trends in Biochemical Sciences. 2006 31:76-78. doi: 10.1016/j.tibs.2005.12.006
PMID: 16406633

SDR goes SGC: A structural genomics initiative
Oppermann, U; Kavanagh, K; Guo, KD; Ng, S; Lukacik, P; Wu, XQ; Dubinina, E; Shafqat, N; Bray, J; Marsden, B; Sharma, S; Vedadi, M; von Delft, F; Sundstrom, M;
. 2006 12:235-241. doi:
PMID:

High-throughput structural characterisation of therapeutic protein targets
Marsden, BD; Sundstrom, M; Knapp, S;
Expert Opinion on Drug Discovery. 2006 1:123-136. doi: 10.1517/17460441.1.2.123
PMID:

2005

Structural basis of inhibitor specificity of the human protooncogene proviral insertion site in moloney murine leukemia virus (PIM-1) kinase.
Bullock, AN; Debreczeni, JE; Fedorov, OY; Nelson, A; Marsden, BD; Knapp, S;
Journal of Medicinal Chemistry. 2005 48:7604-7614. doi:
PMID: 16302800

Enzymology and Molecular Biology of Carbonyl Metabolism
Marsden, B; Oppermann, U; Kavanagh, K; Guo, K; Ng, S; Lukacik, P; Wu, X; Dubinia, E; Shafqat, N; Bray, J; Sharma, S; Vedadi, M;
. 2005 12:-. doi:
PMID:

2002

A novel allelic variant of the human TSG-6 gene encoding an amino acid difference in the CUB module. Chromosomal localization, frequency analysis, modeling, and expression.
Nentwich, HA; Mustafa, Z; Rugg, MS; Marsden, BD; Cordell, MR; Mahoney, DJ; Jenkins, SC; Dowling, B; Fries, E; Milner, CM; Loughlin, J; Day, AJ;
Journal of Biological Chemistry. 2002 277:15354-15362. doi: 10.1074/jbc.M110765200
PMID: 11854277

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