James Thompson
James Thompson
Research Scientist, Amazon
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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ...
Methods in enzymology 487, 545-574, 2011
Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: four approaches that performed well in CASP8
E Krieger, K Joo, J Lee, J Lee, S Raman, J Thompson, M Tyka, D Baker, ...
Proteins: Structure, Function, and Bioinformatics 77 (S9), 114-122, 2009
High-resolution comparative modeling with RosettaCM
Y Song, F DiMaio, RYR Wang, D Kim, C Miles, TJ Brunette, J Thompson, ...
Structure 21 (10), 1735-1742, 2013
Crystal structure of a monomeric retroviral protease solved by protein folding game players
F Khatib, F DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, ...
Nature structural & molecular biology 18 (10), 1175-1177, 2011
Structure prediction for CASP8 with all‐atom refinement using Rosetta
S Raman, R Vernon, J Thompson, M Tyka, R Sadreyev, J Pei, D Kim, ...
Proteins: Structure, Function, and Bioinformatics 77 (S9), 89-99, 2009
Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@ home
R Das, B Qian, S Raman, R Vernon, J Thompson, P Bradley, S Khare, ...
Proteins: Structure, Function, and Bioinformatics 69 (S8), 118-128, 2007
Scientific benchmarks for guiding macromolecular energy function improvement
A Leaver-Fay, MJ O'meara, M Tyka, R Jacak, Y Song, EH Kellogg, ...
Methods in enzymology 523, 109-143, 2013
The experience of illness
R Fitzpatrick, J Hinton, S Newman, G Scambler, J Thompson
Routledge, 1984
Five novel loci for inherited hearing loss mapped by SNP-based homozygosity profiles in Palestinian families
H Shahin, T Walsh, AA Rayyan, MK Lee, J Higgins, D Dickel, K Lewis, ...
European Journal of Human Genetics 18 (4), 407-413, 2010
Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway
WS Mak, S Tran, R Marcheschi, S Bertolani, J Thompson, D Baker, ...
Nature communications 6 (1), 10005, 2015
High-resolution μCT of a mouse embryo using a compact laser-driven X-ray betatron source
JM Cole, DR Symes, NC Lopes, JC Wood, K Poder, S Alatabi, ...
Proceedings of the National Academy of Sciences 115 (25), 6335-6340, 2018
Structure‐guided forcefield optimization
Y Song, M Tyka, A Leaver‐Fay, J Thompson, D Baker
Proteins: Structure, Function, and Bioinformatics 79 (6), 1898-1909, 2011
Incorporation of evolutionary information into Rosetta comparative modeling
J Thompson, D Baker
Proteins: Structure, Function, and Bioinformatics 79 (8), 2380-2388, 2011
Accurate protein structure modeling using sparse NMR data and homologous structure information
JM Thompson, NG Sgourakis, G Liu, P Rossi, Y Tang, JL Mills, ...
Proceedings of the National Academy of Sciences 109 (25), 9875-9880, 2012
APOBEC2 is a monomer in solution: implications for APOBEC3G models
TC Krzysiak, J Jung, J Thompson, D Baker, AM Gronenborn
Biochemistry 51 (9), 2008-2017, 2012
Genetic algorithm learning as a robust approach to RNA editing site prediction
J Thompson, S Gopal
BMC bioinformatics 7, 1-12, 2006
Janus: prediction and ranking of mutations required for functional interconversion of enzymes
TA Addington, RW Mertz, JB Siegel, JM Thompson, AJ Fisher, V Filkov, ...
Journal of molecular biology 425 (8), 1378-1389, 2013
High-resolution structure of a retroviral protease folded as a monomer
M Gilski, M Kazmierczyk, S Krzywda, H Zábranská, S Cooper, Z Popović, ...
Acta Crystallographica Section D: Biological Crystallography 67 (11), 907-914, 2011
Phylogenetic fate mapping: theoretical and experimental studies applied to the development of mouse fibroblasts
SJ Salipante, JM Thompson, MS Horwitz
Genetics 178 (2), 967-977, 2008
Rosetta in CAPRI rounds 13–19
SJ Fleishman, JE Corn, EM Strauch, TA Whitehead, I Andre, J Thompson, ...
Proteins: Structure, Function, and Bioinformatics 78 (15), 3212-3218, 2010
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