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
2084 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
1526 2009 Inceptionism: Going deeper into neural networks A Mordvintsev, C Olah, M Tyka
Google research blog 20 (14), 5, 2015
812 2015 Algorithm discovery by protein folding game players F Khatib, S Cooper, MD Tyka, K Xu, I Makedon, Z Popović, D Baker, ...
Proceedings of the National Academy of Sciences 108 (47), 18949-18953, 2011
683 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
599 2009 Relaxation of backbone bond geometry improves protein energy landscape modeling P Conway, MD Tyka, F DiMaio, DE Konerding, D Baker
Protein science 23 (1), 47-55, 2014
421 2014 Alternate states of proteins revealed by detailed energy landscape mapping MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ...
Journal of molecular biology 405 (2), 607-618, 2011
386 2011 High-precision automated reconstruction of neurons with flood-filling networks M Januszewski, J Kornfeld, PH Li, A Pope, T Blakely, L Lindsey, ...
Nature methods 15 (8), 605-610, 2018
370 2018 Refinement of protein structures into low-resolution density maps using rosetta F DiMaio, MD Tyka, ML Baker, W Chiu, D Baker
Journal of molecular biology 392 (1), 181-190, 2009
328 2009 NMR structure determination for larger proteins using backbone-only data S Raman, OF Lange, P Rossi, M Tyka, X Wang, J Aramini, G Liu, ...
Science 327 (5968), 1014-1018, 2010
310 2010 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
284 2007 Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta MJ O’Meara, A Leaver-Fay, MD Tyka, A Stein, K Houlihan, F DiMaio, ...
Journal of chemical theory and computation 11 (2), 609-622, 2015
267 2015 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
254 2013 Deepdream-a code example for visualizing neural networks A Mordvintsev, C Olah, M Tyka
Google Research 2 (5), 67, 2015
172 2015 Principles for computational design of binding antibodies D Baran, MG Pszolla, GD Lapidoth, C Norn, O Dym, T Unger, S Albeck, ...
Proceedings of the National Academy of Sciences 114 (41), 10900-10905, 2017
157 2017 Inceptionism: Going deeper into neural networks, 2015 A Mordvintsev, C Olah, M Tyka
URL https://research. googleblog. com/2015/06/inceptionism-going-deeper-into …, 2015
123 2015 AbDesign : An algorithm for combinatorial backbone design guided by natural conformations and sequencesGD Lapidoth, D Baran, GM Pszolla, C Norn, A Alon, MD Tyka, ...
Proteins: Structure, Function, and Bioinformatics 83 (8), 1385-1406, 2015
121 2015 Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment PH Li, LF Lindsey, M Januszewski, M Tyka, J Maitin-Shepard, T Blakely, ...
Microscopy and Microanalysis 25 (S2), 1364-1365, 2019
97 2019 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
68 2011 Limits and CO J He, MD Tyka
Biogeosciences 20 (1), 27-43, 2023
63 2023 
David BakerUniversity of WashingtonVahvistettu sähköpostiosoite verkkotunnuksessa uw.edu