Michael Tyka
Cited by
Cited by
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
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
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
Inceptionism: Going deeper into neural networks
A Mordvintsev, C Olah, M Tyka
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
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
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
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
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
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
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
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
Deepdream-a code example for visualizing neural networks
A Mordvintsev, C Olah, M Tyka
Google Research 2 (5), 2015
Metal Mater Trans
CY Wang, C Beckermann
A 27, 2754-2764, 1996
An efficient, path-independent method for free-energy calculations
MD Tyka, AR Clarke, RB Sessions
The Journal of Physical Chemistry B 110 (34), 17212-17220, 2006
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
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
AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences
GD Lapidoth, D Baran, GM Pszolla, C Norn, A Alon, MD Tyka, ...
Proteins: Structure, Function, and Bioinformatics 83 (8), 1385-1406, 2015
Prediction of structures of zinc‐binding proteins through explicit modeling of metal coordination geometry
C Wang, R Vernon, O Lange, M Tyka, D Baker
Protein science 19 (3), 494-506, 2010
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