Publications by authors named "Michael Tyka"

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Principles for computational design of binding antibodies.
Dror Baran, M Gabriele Pszolla, Gideon D Lapidoth, Christoffer Norn, Orly Dym, Michael D Tyka

Proc Natl Acad Sci U S A· October 2017

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AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.
Gideon D Lapidoth, Dror Baran, Gabriele M Pszolla, Christoffer Norn, Assaf Alon, Michael D Tyka

Proteins· August 2015

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Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.
Matthew J O'Meara, Andrew Leaver-Fay, Michael D Tyka, Amelie Stein, Kevin Houlihan

J Chem Theory Comput· February 2015

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Relaxation of backbone bond geometry improves protein energy landscape modeling.
Patrick Conway, Michael D Tyka, Frank DiMaio, David E Konerding, David Baker

Protein Sci· January 2014

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Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.
Michael D Tyka, Kenneth Jung, David Baker

J Comput Chem· December 2012

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Modeling disordered regions in proteins using Rosetta.
Ray Yu-Ruei Wang, Yan Han, Kristina Krassovsky, William Sheffler, Michael Tyka

PLoS One· December 2011

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Algorithm discovery by protein folding game players.
Firas Khatib, Seth Cooper, Michael D Tyka, Kefan Xu, Ilya Makedon

Proc Natl Acad Sci U S A· November 2011

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Structure-guided forcefield optimization.
Yifan Song, Michael Tyka, Andrew Leaver-Fay, James Thompson, David Baker

Proteins· June 2011

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Andrew Leaver-Fay, Michael Tyka, Steven M Lewis, Oliver F Lange, James Thompson

Methods Enzymol· April 2011

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Alternate states of proteins revealed by detailed energy landscape mapping.
Michael D Tyka, Daniel A Keedy, Ingemar André, Frank Dimaio, Yifan Song

J Mol Biol· January 2011

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Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.
Chu Wang, Robert Vernon, Oliver Lange, Michael Tyka, David Baker

Protein Sci· March 2010

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NMR structure determination for larger proteins using backbone-only data.
Srivatsan Raman, Oliver F Lange, Paolo Rossi, Michael Tyka, Xu Wang

Science· February 2010

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Structure prediction for CASP8 with all-atom refinement using Rosetta.
Srivatsan Raman, Robert Vernon, James Thompson, Michael Tyka, Ruslan Sadreyev

Proteins· January 2010

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Refinement of protein structures into low-resolution density maps using rosetta.
Frank DiMaio, Michael D Tyka, Matthew L Baker, Wah Chiu, David Baker

J Mol Biol· September 2009

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Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Rhiju Das, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Michael D Tyka

Proteins· January 2008

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Absolute free-energy calculations of liquids using a harmonic reference state.
Michael D Tyka, Richard B Sessions, Anthony R Clarke

J Phys Chem B· August 2007

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An efficient, path-independent method for free-energy calculations.
Michael D Tyka, Anthony R Clarke, Richard B Sessions

J Phys Chem B· August 2006

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