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Items: 1 to 50 of 182

1.

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions.

Ramsbottom KA, Carr DF, Jones AR, Rigden DJ.

Mol Immunol. 2018 Sep;101:488-499. doi: 10.1016/j.molimm.2018.08.003. Epub 2018 Aug 18.

2.

SIMBAD: a sequence-independent molecular-replacement pipeline.

Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Wu R, Sanishvili R, Xu Y, Lisa MN, Buschiazzo A, Shepard W, Rigden DJ, Keegan RM.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):595-605. doi: 10.1107/S2059798318005752. Epub 2018 Jun 8.

3.

Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance.

Isaacs AT, Mawejje HD, Tomlinson S, Rigden DJ, Donnelly MJ.

BMC Genomics. 2018 Mar 27;19(1):225. doi: 10.1186/s12864-018-4605-1.

4.

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.

Rigden DJ, Thomas JMH, Simkovic F, Simpkin A, Winn MD, Mayans O, Keegan RM.

Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):183-193. doi: 10.1107/S2059798318002310. Epub 2018 Mar 2.

5.

Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.

Keegan RM, McNicholas SJ, Thomas JMH, Simpkin AJ, Simkovic F, Uski V, Ballard CC, Winn MD, Wilson KS, Rigden DJ.

Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):167-182. doi: 10.1107/S2059798318003455. Epub 2018 Mar 6.

6.

Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae.

Weetman D, Wilding CS, Neafsey DE, Müller P, Ochomo E, Isaacs AT, Steen K, Rippon EJ, Morgan JC, Mawejje HD, Rigden DJ, Okedi LM, Donnelly MJ.

Sci Rep. 2018 Feb 13;8(1):2920. doi: 10.1038/s41598-018-21265-5.

7.

Autophosphorylation Is a Mechanism of Inhibition in Twitchin Kinase.

Williams RM, Franke B, Wilkinson M, Fleming JR, Rigden DJ, Benian GM, Eyers PA, Mayans O.

J Mol Biol. 2018 Mar 16;430(6):793-805. doi: 10.1016/j.jmb.2018.01.020. Epub 2018 Feb 3.

PMID:
29408381
8.

Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds.

Kozic M, Fox SJ, Thomas JM, Verma CS, Rigden DJ.

Proteins. 2018 May;86(5):548-565. doi: 10.1002/prot.25473. Epub 2018 Feb 18.

PMID:
29388242
9.

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

Rigden DJ, Fernández XM.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1-D7. doi: 10.1093/nar/gkx1235.

10.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ.

Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):985-996. doi: 10.1107/S2059798317016436. Epub 2017 Nov 22.

11.

Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of Trypanosoma cruzi.

Rojas-Pirela M, Rigden DJ, Michels PA, Cáceres AJ, Concepción JL, Quiñones W.

Mol Biochem Parasitol. 2018 Jan;219:52-66. doi: 10.1016/j.molbiopara.2017.11.002. Epub 2017 Nov 11. Review.

PMID:
29133150
12.

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus.

Loxley GM, Unsworth J, Turton MJ, Jebb A, Lilley KS, Simpson DM, Rigden DJ, Hurst JL, Beynon RJ.

Open Biol. 2017 Sep;7(9). pii: 170135. doi: 10.1098/rsob.170135.

13.

Novel compound heterozygous ASXL3 mutation causing Bainbridge-ropers like syndrome and primary IGF1 deficiency.

Giri D, Rigden D, Didi M, Peak M, McNamara P, Senniappan S.

Int J Pediatr Endocrinol. 2017;2017:8. doi: 10.1186/s13633-017-0047-9. Epub 2017 Aug 4.

14.

Applications of contact predictions to structural biology.

Simkovic F, Ovchinnikov S, Baker D, Rigden DJ.

IUCrJ. 2017 Apr 18;4(Pt 3):291-300. doi: 10.1107/S2052252517005115. eCollection 2017 May 1. Review.

15.

ConKit: a python interface to contact predictions.

Simkovic F, Thomas JMH, Rigden DJ.

Bioinformatics. 2017 Jul 15;33(14):2209-2211. doi: 10.1093/bioinformatics/btx148.

16.
17.

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 May 19;45(9):5627. doi: 10.1093/nar/gkx021. No abstract available.

18.

Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population.

Carr DF, Bourgeois S, Chaponda M, Takeshita LY, Morris AP, Castro EM, Alfirevic A, Jones AR, Rigden DJ, Haldenby S, Khoo S, Lalloo DG, Heyderman RS, Dandara C, Kampira E, van Oosterhout JJ, Ssali F, Munderi P, Novelli G, Borgiani P, Nelson MR, Holden A, Deloukas P, Pirmohamed M.

J Antimicrob Chemother. 2017 Apr 1;72(4):1152-1162. doi: 10.1093/jac/dkw545.

19.

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

Galperin MY, Fernández-Suárez XM, Rigden DJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1-D11. doi: 10.1093/nar/gkw1188. Erratum in: Nucleic Acids Res. 2017 May 19;45(9):5627.

21.

The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability.

Heride C, Rigden DJ, Bertsoulaki E, Cucchi D, De Smaele E, Clague MJ, Urbé S.

J Cell Sci. 2016 Nov 1;129(21):4001-4013. Epub 2016 Sep 12.

22.

Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I.

Bogomolovas J, Fleming JR, Anderson BR, Williams R, Lange S, Simon B, Khan MM, Rudolf R, Franke B, Bullard B, Rigden DJ, Granzier H, Labeit S, Mayans O.

Open Biol. 2016 Sep;6(9). pii: 160114.

23.

CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex.

Zhou T, Fleming JR, Franke B, Bogomolovas J, Barsukov I, Rigden DJ, Labeit S, Mayans O.

FEBS Lett. 2016 Sep;590(18):3098-110. doi: 10.1002/1873-3468.12362. Epub 2016 Sep 2.

24.

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

Simkovic F, Thomas JM, Keegan RM, Winn MD, Mayans O, Rigden DJ.

IUCrJ. 2016 Jun 15;3(Pt 4):259-70. doi: 10.1107/S2052252516008113. eCollection 2016 Jul 1.

25.

GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ.

Simpkin AJ, Rigden DJ.

BMC Res Notes. 2016 Jul 13;9:343. doi: 10.1186/s13104-016-2149-5.

26.

Potential DNA binding and nuclease functions of ComEC domains characterized in silico.

Baker JA, Simkovic F, Taylor HM, Rigden DJ.

Proteins. 2016 Oct;84(10):1431-42. doi: 10.1002/prot.25088. Epub 2016 Jul 1.

27.

The industrial melanism mutation in British peppered moths is a transposable element.

Van't Hof AE, Campagne P, Rigden DJ, Yung CJ, Lingley J, Quail MA, Hall N, Darby AC, Saccheri IJ.

Nature. 2016 Jun 2;534(7605):102-5. doi: 10.1038/nature17951.

PMID:
27251284
28.

The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

Rigden DJ, Fernández-Suárez XM, Galperin MY.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1-6. doi: 10.1093/nar/gkv1356.

29.

Structural advances on titin: towards an atomic understanding of multi-domain functions in myofilament mechanics and scaffolding.

Zacharchenko T, von Castelmur E, Rigden DJ, Mayans O.

Biochem Soc Trans. 2015 Oct;43(5):850-5. doi: 10.1042/BST20150084. Review.

PMID:
26517893
30.

Transcriptomic analysis of Shiga-toxigenic bacteriophage carriage reveals a profound regulatory effect on acid resistance in Escherichia coli.

Veses-Garcia M, Liu X, Rigden DJ, Kenny JG, McCarthy AJ, Allison HE.

Appl Environ Microbiol. 2015 Dec;81(23):8118-25. doi: 10.1128/AEM.02034-15. Epub 2015 Sep 18.

31.

ATG24 Represses Autophagy and Differentiation and Is Essential for Homeostasy of the Flagellar Pocket in Trypanosoma brucei.

Brennand A, Rico E, Rigden DJ, Van Der Smissen P, Courtoy PJ, Michels PA.

PLoS One. 2015 Jun 19;10(6):e0130365. doi: 10.1371/journal.pone.0130365. eCollection 2015.

32.

Routine phasing of coiled-coil protein crystal structures with AMPLE.

Thomas JM, Keegan RM, Bibby J, Winn MD, Mayans O, Rigden DJ.

IUCrJ. 2015 Feb 26;2(Pt 2):198-206. doi: 10.1107/S2052252515002080. eCollection 2015 Mar 1.

33.

Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae.

Weetman D, Mitchell SN, Wilding CS, Birks DP, Yawson AE, Essandoh J, Mawejje HD, Djogbenou LS, Steen K, Rippon EJ, Clarkson CS, Field SG, Rigden DJ, Donnelly MJ.

Mol Ecol. 2015 Jun;24(11):2656-72. doi: 10.1111/mec.13197. Epub 2015 May 14.

34.

Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22.

Sohn YS, Shin HC, Park WS, Ge J, Kim CH, Lee BL, Heo WD, Jung JU, Rigden DJ, Oh BH.

PLoS One. 2015 Mar 30;10(3):e0118683. doi: 10.1371/journal.pone.0118683. eCollection 2015.

35.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ.

Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):338-43. doi: 10.1107/S1399004714025784. Epub 2015 Jan 23.

36.

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

Galperin MY, Rigden DJ, Fernández-Suárez XM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1-5. doi: 10.1093/nar/gku1241.

37.

Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in Neurospora crassa.

Gonçalves AP, Monteiro J, Lucchi C, Kowbel DJ, Cordeiro JM, Correia-de-Sá P, Rigden DJ, Glass NL, Videira A.

Microb Cell. 2014 Aug 9;1(9):289-302. doi: 10.15698/mic2014.09.165.

38.

Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution.

Brown RW, Collingridge PW, Gull K, Rigden DJ, Ginger ML.

PLoS One. 2014 Jul 22;9(7):e103026. doi: 10.1371/journal.pone.0103026. eCollection 2014.

39.

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.

Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A.

BMC Bioinformatics. 2014 Jun 17;15:196. doi: 10.1186/1471-2105-15-196.

40.

Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line.

Bogomolovas J, Gasch A, Simkovic F, Rigden DJ, Labeit S, Mayans O.

Open Biol. 2014 May;4(5):140041. doi: 10.1098/rsob.140041.

41.

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.

Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A.

BMC Bioinformatics. 2014 Apr 17;15:112. doi: 10.1186/1471-2105-15-112.

42.

Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae.

Mitchell SN, Rigden DJ, Dowd AJ, Lu F, Wilding CS, Weetman D, Dadzie S, Jenkins AM, Regna K, Boko P, Djogbenou L, Muskavitch MA, Ranson H, Paine MJ, Mayans O, Donnelly MJ.

PLoS One. 2014 Mar 27;9(3):e92662. doi: 10.1371/journal.pone.0092662. eCollection 2014.

43.

Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1.

Franke B, Gasch A, Rodriguez D, Chami M, Khan MM, Rudolf R, Bibby J, Hanashima A, Bogomolovas J, von Castelmur E, Rigden DJ, Uson I, Labeit S, Mayans O.

Open Biol. 2014 Mar 26;4:130172. doi: 10.1098/rsob.130172.

44.

The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.

Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND.

Version 2. F1000Res. 2013 Jul 10 [revised 2013 Jan 1];2:154. doi: 10.12688/f1000research.2-154.v2. eCollection 2013.

45.

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

Fernández-Suárez XM, Rigden DJ, Galperin MY.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1-6. doi: 10.1093/nar/gkt1282. Epub 2013 Dec 6.

46.

Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis.

Hotta K, Keegan RM, Ranganathan S, Fang M, Bibby J, Winn MD, Sato M, Lian M, Watanabe K, Rigden DJ, Kim CY.

Angew Chem Int Ed Engl. 2014 Jan 13;53(3):824-8.

PMID:
24302672
47.

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement.

Bibby J, Keegan RM, Mayans O, Winn MD, Rigden DJ.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2194-201. doi: 10.1107/S0907444913018453. Epub 2013 Oct 12.

48.

Crystal structure of the nipah virus phosphoprotein tetramerization domain.

Bruhn JF, Barnett KC, Bibby J, Thomas JM, Keegan RM, Rigden DJ, Bornholdt ZA, Saphire EO.

J Virol. 2014 Jan;88(1):758-62. doi: 10.1128/JVI.02294-13. Epub 2013 Oct 23.

49.

Ubiquitination of the glycosomal matrix protein receptor PEX5 in Trypanosoma brucei by PEX4 displays novel features.

Gualdrón-López M, Chevalier N, Van Der Smissen P, Courtoy PJ, Rigden DJ, Michels PAM.

Biochim Biophys Acta. 2013 Dec;1833(12):3076-3092. doi: 10.1016/j.bbamcr.2013.08.008. Epub 2013 Aug 27.

50.

Deubiquitylases from genes to organism.

Clague MJ, Barsukov I, Coulson JM, Liu H, Rigden DJ, Urbé S.

Physiol Rev. 2013 Jul;93(3):1289-315. doi: 10.1152/physrev.00002.2013. Review.

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