ArticleProceedings of the National Academy of Sciences of the United States of America2012
Modeling and design by hierarchical natural moves.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- Quantitative approaches for decoding the specificity of the human T cell repertoire.Frontiers in immunology · 2023Review
- Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities.RNA (New York, N.Y.) · 2020Article
- HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.Journal of chemical information and modeling · 2019Article
- Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.International journal of computational biology and drug design · 2018Article
- Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering.Journal of molecular biology · 2017Article
- Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.Nucleic acids research · 2017Article
- SimGen: A General Simulation Method for Large Systems.Journal of molecular biology · 2017Article
- Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.Frontiers in molecular biosciences · 2017Article
- Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations.Computational biology and chemistry · 2016Article
- Modeling Functional Motions of Biological Systems by Customized Natural Moves.Biophysical journal · 2016Article
- SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.Nucleic acids research · 2016Article
- Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.Bioinformatics (Oxford, England) · 2016Article
- MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.Nucleic acids research · 2016Article
- GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.PloS one · 2015Article
- Characterizing RNA ensembles from NMR data with kinematic models.Nucleic acids research · 2014Article
- Computational and experimental characterization of RNA cubic nanoscaffolds.Methods (San Diego, Calif.) · 2014Article
- Graph-based sampling for approximating global helical topologies of RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- SIMS: a hybrid method for rapid conformational analysis.PloS one · 2013Article
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3 authors.
Funding
Abstract
We develop a unique algorithm implemented in the program MOSAICS (Methodologies for Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling without compromising the resolution of interest. This is achieved by modeling with customizable hierarchical degrees of freedom, thereby circumventing major limitations of conventional molecular modeling. With the emergence of RNA-based nanotechnology, large RNAs in all-atom representation are used here to benchmark our algorithm. Our method locates all favorable structural states of a model RNA of significant complexity while improving sampling accuracy and increasing speed many fold over existing all-atom RNA modeling methods. We also modeled the effects of sequence mutations on the structural building blocks of tRNA-based nanotechnology. With its flexibility in choosing arbitrary degrees of freedom as well as in allowing different all-atom energy functions, MOSAICS is an ideal tool to model and design biomolecules of the nanoscale.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.