☰

James Thompson - Publications

Affiliations: 
2011 University of Washington, Seattle, Seattle, WA 
Tree Info Similar researchers PubMed Report error

17 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 7: 11912. PMID 27271283 DOI: 10.1038/Ncomms11912  0.591
2015 Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 6: 10005. PMID 26598135 DOI: 10.1038/Ncomms10005  0.595
2013 Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. High-resolution comparative modeling with RosettaCM. Structure (London, England : 1993). 21: 1735-42. PMID 24035711 DOI: 10.1016/J.Str.2013.08.005  0.716
2013 Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0  0.713
2013 Addington TA, Mertz RW, Siegel JB, Thompson JM, Fisher AJ, Filkov V, Fleischman NM, Suen AA, Zhang C, Toney MD. Janus: prediction and ranking of mutations required for functional interconversion of enzymes. Journal of Molecular Biology. 425: 1378-89. PMID 23396064 DOI: 10.1016/J.Jmb.2013.01.034  0.548
2012 Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. Accurate protein structure modeling using sparse NMR data and homologous structure information. Proceedings of the National Academy of Sciences of the United States of America. 109: 9875-80. PMID 22665781 DOI: 10.1073/Pnas.1202485109  0.68
2012 Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM. APOBEC2 is a monomer in solution: Implications for APOBEC3G Models Biochemistry. 51: 2008-2017. PMID 22339232 DOI: 10.1021/Bi300021S  0.416
2011 Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M. High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallographica. Section D, Biological Crystallography. 67: 907-14. PMID 22101816 DOI: 10.1107/S0907444911035943  0.699
2011 Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology. 18: 1175-7. PMID 21926992 DOI: 10.1038/Nsmb.2119  0.708
2011 Thompson J, Baker D. Incorporation of evolutionary information into Rosetta comparative modeling. Proteins. 79: 2380-8. PMID 21638331 DOI: 10.1002/Prot.23046  0.508
2011 Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure-guided forcefield optimization. Proteins. 79: 1898-909. PMID 21488100 DOI: 10.1002/Prot.23013  0.754
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  0.666
2010 Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/Prot.22784  0.756
2009 Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77: 114-22. PMID 19768677 DOI: 10.1002/Prot.22570  0.65
2009 Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540  0.764
2007 Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636  0.696
2002 Thompson JB, Hansma HG, Hansma PK, Plaxco KW. The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy. Journal of Molecular Biology. 322: 645-52. PMID 12225756 DOI: 10.1016/S0022-2836(02)00801-X  0.492
Show low-probability matches.