Attenuating dependence on structural data in computing protein energy landscapes
暂无分享,去创建一个
Erion Plaku | Amarda Shehu | Tatiana Maximova | David Morris | E. Plaku | Amarda Shehu | T. Maximova | David Morris
[1] A. D. McLachlan,et al. A mathematical procedure for superimposing atomic coordinates of proteins , 1972 .
[2] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[3] Erion Plaku,et al. Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants , 2017, BCB.
[4] Amarda Shehu,et al. From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[5] Erion Plaku,et al. A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic , 2016, J. Artif. Intell. Res..
[6] Ruth Nussinov,et al. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics , 2016, PLoS Comput. Biol..
[7] Amarda Shehu,et al. Computing energy landscape maps and structural excursions of proteins , 2016, BMC Genomics.
[8] Ivet Bahar,et al. Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model , 2014, PLoS Comput. Biol..
[9] Erion Plaku,et al. Sample-based Models of Protein Structural Transitions , 2016, BCB.
[10] Ruth Nussinov,et al. A second molecular biology revolution? The energy landscapes of biomolecular function. , 2014, Physical chemistry chemical physics : PCCP.
[11] Pemra Doruker,et al. Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes. , 2008, Biophysical journal.
[12] James Andrew McCammon,et al. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics , 2009, PLoS Comput. Biol..
[13] I. Bahar,et al. Global dynamics of proteins: bridging between structure and function. , 2010, Annual review of biophysics.
[14] T. Siméon,et al. Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods , 2013, BMC Structural Biology.
[15] Amarda Shehu,et al. A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes , 2015, J. Comput. Biol..
[16] Daniel Russel,et al. The structural dynamics of macromolecular processes. , 2009, Current opinion in cell biology.
[17] R. Nussinov,et al. The role of dynamic conformational ensembles in biomolecular recognition. , 2009, Nature chemical biology.
[18] Michael Palmgren,et al. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana , 2016, BMC Genomics.
[19] Leo S. D. Caves,et al. Bio3d: An R Package , 2022 .
[20] Erion Plaku,et al. Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data , 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[21] G. Chirikjian,et al. Iterative cluster‐NMA: A tool for generating conformational transitions in proteins , 2009, Proteins.
[22] Ruth Nussinov,et al. Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm , 2015, PLoS Comput. Biol..
[23] Erion Plaku,et al. Structure-Guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.