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Items: 50

1.

Computational discovery of direct associations between GO terms and protein domains.

Alborzi SZ, Ritchie DW, Devignes MD.

BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):413. doi: 10.1186/s12859-018-2380-2.

2.

PDB-wide identification of biological assemblies from conserved quaternary structure geometry.

Dey S, Ritchie DW, Levy ED.

Nat Methods. 2018 Jan;15(1):67-72. doi: 10.1038/nmeth.4510. Epub 2017 Nov 20.

PMID:
29155427
3.

ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.

Alborzi SZ, Devignes MD, Ritchie DW.

BMC Bioinformatics. 2017 Feb 13;18(1):107. doi: 10.1186/s12859-017-1519-x.

4.

Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.

El Houasli M, Maigret B, Devignes MD, Ghoorah AW, Grudinin S, Ritchie DW.

Proteins. 2017 Mar;85(3):463-469. doi: 10.1002/prot.25182. Epub 2016 Oct 24.

PMID:
27701764
5.

PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation.

Neveu E, Ritchie DW, Popov P, Grudinin S.

Bioinformatics. 2016 Sep 1;32(17):i693-i701. doi: 10.1093/bioinformatics/btw443.

PMID:
27587691
6.

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.

Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B, Mottarella SE, Kholodov Y, Ritchie DW, Vajda S, Kozakov D.

Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4286-93. doi: 10.1073/pnas.1603929113. Epub 2016 Jul 13.

7.

Calculating and scoring high quality multiple flexible protein structure alignments.

Ritchie DW.

Bioinformatics. 2016 Sep 1;32(17):2650-8. doi: 10.1093/bioinformatics/btw300. Epub 2016 May 13.

PMID:
27187202
8.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

9.

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Methods Mol Biol. 2016;1415:91-105. doi: 10.1007/978-1-4939-3572-7_5.

PMID:
27115629
10.

GESSE: Predicting Drug Side Effects from Drug-Target Relationships.

Pérez-Nueno VI, Souchet M, Karaboga AS, Ritchie DW.

J Chem Inf Model. 2015 Sep 28;55(9):1804-23. doi: 10.1021/acs.jcim.5b00120. Epub 2015 Aug 26.

PMID:
26251970
11.

Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex.

Bourquard T, Landomiel F, Reiter E, Crépieux P, Ritchie DW, Azé J, Poupon A.

Sci Rep. 2015 Jun 1;5:10760. doi: 10.1038/srep10760.

12.

A structure-based classification and analysis of protein domain family binding sites and their interactions.

Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW.

Biology (Basel). 2015 Apr 9;4(2):327-43. doi: 10.3390/biology4020327.

13.

GES polypharmacology fingerprints: a novel approach for drug repositioning.

Pérez-Nueno VI, Karaboga AS, Souchet M, Ritchie DW.

J Chem Inf Model. 2014 Mar 24;54(3):720-34. doi: 10.1021/ci4006723. Epub 2014 Feb 17.

PMID:
24494653
14.

KBDOCK 2013: a spatial classification of 3D protein domain family interactions.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D389-95. doi: 10.1093/nar/gkt1199. Epub 2013 Nov 23.

15.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

16.

gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.

Hoang TV, Cavin X, Schultz P, Ritchie DW.

BMC Struct Biol. 2013 Oct 21;13:25. doi: 10.1186/1472-6807-13-25.

17.

Protein docking using case-based reasoning.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Proteins. 2013 Dec;81(12):2150-8. doi: 10.1002/prot.24433.

PMID:
24123156
18.

gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.

Hoang TV, Cavin X, Ritchie DW.

J Struct Biol. 2013 Nov;184(2):348-54. doi: 10.1016/j.jsb.2013.09.010. Epub 2013 Sep 21.

PMID:
24060989
19.

DockTrina: docking triangular protein trimers.

Popov P, Ritchie DW, Grudinin S.

Proteins. 2014 Jan;82(1):34-44. doi: 10.1002/prot.24344. Epub 2013 Aug 31.

PMID:
23775700
20.

Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology.

Carrieri A, Pérez-Nueno VI, Lentini G, Ritchie DW.

Curr Top Med Chem. 2013;13(9):1069-97. Review.

PMID:
23651484
21.

Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity.

Ritchie DW, Ghoorah AW, Mavridis L, Venkatraman V.

Bioinformatics. 2012 Dec 15;28(24):3274-81. doi: 10.1093/bioinformatics/bts618. Epub 2012 Oct 23.

PMID:
23093609
22.

Recent trends and applications in 3D virtual screening.

Ghemtio L, Perez-Nueno VI, Leroux V, Asses Y, Souchet M, Mavridis L, Maigret B, Ritchie DW.

Comb Chem High Throughput Screen. 2012 Nov;15(9):749-69. Review.

PMID:
22934947
23.

Detecting drug promiscuity using Gaussian ensemble screening.

Pérez-Nueno VI, Venkatraman V, Mavridis L, Ritchie DW.

J Chem Inf Model. 2012 Aug 27;52(8):1948-61. doi: 10.1021/ci3000979. Epub 2012 Jul 19.

PMID:
22747187
24.

Flexible protein docking refinement using pose-dependent normal mode analysis.

Venkatraman V, Ritchie DW.

Proteins. 2012 Aug;80(9):2262-74. doi: 10.1002/prot.24115. Epub 2012 Jun 18.

PMID:
22610423
25.

Identifying and characterizing promiscuous targets: implications for virtual screening.

Pérez-Nueno VI, Ritchie DW.

Expert Opin Drug Discov. 2012 Jan;7(1):1-17. doi: 10.1517/17460441.2011.632406. Epub 2011 Nov 8. Review.

PMID:
22468890
26.

Exploring c-Met kinase flexibility by sampling and clustering its conformational space.

Asses Y, Venkatraman V, Leroux V, Ritchie DW, Maigret B.

Proteins. 2012 Apr;80(4):1227-38. doi: 10.1002/prot.24021. Epub 2012 Jan 24.

PMID:
22275094
27.

Representing and comparing protein folds and fold families using three-dimensional shape-density representations.

Mavridis L, Ghoorah AW, Venkatraman V, Ritchie DW.

Proteins. 2012 Feb;80(2):530-45. doi: 10.1002/prot.23218. Epub 2011 Nov 12.

PMID:
22081520
28.

Spatial clustering of protein binding sites for template based protein docking.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Bioinformatics. 2011 Oct 15;27(20):2820-7. doi: 10.1093/bioinformatics/btr493. Epub 2011 Aug 27.

PMID:
21873637
29.

Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening.

Pérez-Nueno VI, Ritchie DW.

J Chem Inf Model. 2011 Jun 27;51(6):1233-48. doi: 10.1021/ci100492r. Epub 2011 Jun 4.

PMID:
21604699
30.

Using Spherical Harmonic Surface Property Representations for Ligand-Based Virtual Screening.

Pérez-Nueno VI, Venkatraman V, Mavridis L, Clark T, Ritchie DW.

Mol Inform. 2011 Mar 14;30(2-3):151-9. doi: 10.1002/minf.201000149. Epub 2010 Dec 22.

PMID:
27466769
31.

Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods.

Venkatraman V, Pérez-Nueno VI, Mavridis L, Ritchie DW.

J Chem Inf Model. 2010 Dec 27;50(12):2079-93. doi: 10.1021/ci100263p. Epub 2010 Nov 23.

PMID:
21090728
32.

Ultra-fast FFT protein docking on graphics processors.

Ritchie DW, Venkatraman V.

Bioinformatics. 2010 Oct 1;26(19):2398-405. doi: 10.1093/bioinformatics/btq444. Epub 2010 Aug 4.

PMID:
20685958
33.

Using graphics processors to accelerate protein docking calculations.

Ritchie DW, Venkatraman V, Mavridis L.

Stud Health Technol Inform. 2010;159:146-55.

PMID:
20543434
34.

HexServer: an FFT-based protein docking server powered by graphics processors.

Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W445-9. doi: 10.1093/nar/gkq311. Epub 2010 May 5.

36.

Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection.

Ferraresso S, Kuhl H, Milan M, Ritchie DW, Secombes CJ, Reinhardt R, Bargelloni L.

Immunogenetics. 2009 Dec;61(11-12):773-88. doi: 10.1007/s00251-009-0398-3. Epub 2009 Nov 19.

37.

Biological profiling of anti-HIV agents and insight into CCR5 antagonist binding using in silico techniques.

Carrieri A, Pérez-Nueno VI, Fano A, Pistone C, Ritchie DW, Teixidó J.

ChemMedChem. 2009 Jul;4(7):1153-63. doi: 10.1002/cmdc.200900101.

PMID:
19544518
38.

Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening.

Pérez-Nueno VI, Pettersson S, Ritchie DW, Borrell JI, Teixidó J.

J Chem Inf Model. 2009 Apr;49(4):810-23. doi: 10.1021/ci800468q.

PMID:
19358515
39.
40.

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.

Ritchie DW, Kozakov D, Vajda S.

Bioinformatics. 2008 Sep 1;24(17):1865-73. doi: 10.1093/bioinformatics/btn334. Epub 2008 Jun 30.

41.

Recent progress and future directions in protein-protein docking.

Ritchie DW.

Curr Protein Pept Sci. 2008 Feb;9(1):1-15. Review.

PMID:
18336319
42.

Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking.

Pérez-Nueno VI, Ritchie DW, Rabal O, Pascual R, Borrell JI, Teixidó J.

J Chem Inf Model. 2008 Mar;48(3):509-33. doi: 10.1021/ci700415g. Epub 2008 Feb 26.

PMID:
18298095
43.

Toward high throughput 3D virtual screening using spherical harmonic surface representations.

Mavridis L, Hudson BD, Ritchie DW.

J Chem Inf Model. 2007 Sep-Oct;47(5):1787-96. Epub 2007 Sep 7.

PMID:
17824600
45.

Docking essential dynamics eigenstructures.

Mustard D, Ritchie DW.

Proteins. 2005 Aug 1;60(2):269-74.

PMID:
15981272
46.
47.
48.

Terminating eukaryote translation: domain 1 of release factor eRF1 functions in stop codon recognition.

Bertram G, Bell HA, Ritchie DW, Fullerton G, Stansfield I.

RNA. 2000 Sep;6(9):1236-47.

49.

Protein docking using spherical polar Fourier correlations.

Ritchie DW, Kemp GJ.

Proteins. 2000 May 1;39(2):178-94.

PMID:
10737939
50.

Modelling antibody side chain conformations using heuristic database search.

Ritchie DW, Kemp GJ.

Proc Int Conf Intell Syst Mol Biol. 1997;5:237-40.

PMID:
9322043

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