Protein structure prediction using Rosetta in CASP12
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Frank DiMaio | Hahnbeom Park | David Baker | Sergey Ovchinnikov | David E Kim | David E. Kim | D. Baker | Hahnbeom Park | S. Ovchinnikov | F. DiMaio | D. Baker
[1] Chaok Seok,et al. Refinement of unreliable local regions in template‐based protein models , 2012, Proteins.
[2] David Baker,et al. High-resolution comparative modeling with RosettaCM. , 2013, Structure.
[3] Jacek Blazewicz,et al. SphereGrinder - reference structure-based tool for quality assessment of protein structural models , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[4] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[5] David E. Kim,et al. Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. , 2016, Journal of chemical theory and computation.
[6] Frank DiMaio,et al. CASP11 refinement experiments with ROSETTA , 2016, Proteins.
[7] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[8] David Baker,et al. Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11 , 2016, Proteins.
[9] Vahid Mirjalili,et al. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. , 2013, Journal of chemical theory and computation.
[10] D. Baker,et al. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era , 2013, Proceedings of the National Academy of Sciences.
[11] Georgios A. Pavlopoulos,et al. Protein structure determination using metagenome sequence data , 2017, Science.
[12] David E. Kim,et al. Large-scale determination of previously unsolved protein structures using evolutionary information , 2015, eLife.
[13] Liam J. McGuffin,et al. The PSIPRED protein structure prediction server , 2000, Bioinform..
[14] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[15] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[16] Alberto Perez,et al. Accelerating molecular simulations of proteins using Bayesian inference on weak information , 2015, Proceedings of the National Academy of Sciences.
[17] F. Dimaio,et al. Improved low-resolution crystallographic refinement with Phenix and Rosetta , 2014 .
[18] D. Baker,et al. Relaxation of backbone bond geometry improves protein energy landscape modeling , 2014, Protein science : a publication of the Protein Society.
[19] SödingJohannes. Protein homology detection by HMM--HMM comparison , 2005 .
[20] David E. Kim,et al. Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta , 2016, Proteins.
[21] Matthias J. Brunner,et al. Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement , 2015, Nature Methods.