EXCEED THE SPACE PROVIDED. The overall goal of the Research Resource Multiscale Modeling Tools for Structural Biology is the development and integration of modeling tools for the exploration of multi-resolution models in structural biology. Problems in structural biology require researchers to move between models of low-resolution and detailed atomic models to fully explore and exploit experimental information. Our resource efforts through core and collaborative research programs are focused on the development of new and integrated approaches to multiscale modeling in four primary focus areas: ? Modeling of large-scale assemblies of nucleic acids and proteins with nucleic acids, including the facile transitioning between models at full atomic resolution and low-resolution representations. ? Protein structure prediction and refinement using hybrid methods combining lattice-based Monte Carlo algorithms with force field based methods, including the requisite tools. Computational infrastructure and data bases that facilitate the development of prediction pipelines. ? The development of algorithms, methods and tools to explore large-scale motions that occur during a virus life cycle, i.e. assembly, maturation and infectivity, as well as a web-based infrastructure and data repository for virus structures and derived properties. ? Novel methods and tools to be used by structural biologists employing cryo-EMto build and refine multiscale structural models. Particular focus will be given to the flexible refinement of atomic-level structures into low-resolution data using elastic network normal mode methods. An additional core research effort ties these threads together through the development and distribution of computer codes to make such simulations readily accessible to the scientific community at large. We complement these developments by: ? collaborations that challenge and direct our Core research efforts ? dissemination and distribution of algorithmic and methodological developments through the established distribution mechanisms employed for the widely distributed Amber and CHARMM molecular modeling packages ? continued development of the VIPER """"""""web-base"""""""" for structural virology ? training of biomedical researchers through research and training workshops
| Salmon, Loïc; Ahlstrom, Logan S; Horowitz, Scott et al. (2016) Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc 138:9826-39 |
| Bruno, Paul A; Morriss-Andrews, Alex; Henderson, Andrew R et al. (2016) A Synthetic Loop Replacement Peptide That Blocks Canonical NF-?B Signaling. Angew Chem Int Ed Engl 55:14997-15001 |
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| Rosen, Laura E; Kathuria, Sagar V; Matthews, C Robert et al. (2015) Non-native structure appears in microseconds during the folding of E. coli RNase H. J Mol Biol 427:443-53 |
| Cheng, Shanshan; Brooks 3rd, Charles L (2015) Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. J Mol Biol 427:3613-3624 |
| Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks 3rd, Charles L et al. (2015) CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. J Struct Biol 190:47-55 |
| Ahlstrom, Logan S; Law, Sean M; Dickson, Alex et al. (2015) Multiscale modeling of a conditionally disordered pH-sensing chaperone. J Mol Biol 427:1670-80 |
| Taylor, Kenneth A; Feig, Michael; Brooks 3rd, Charles L et al. (2014) Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. J Struct Biol 185:375-82 |
| Zeng, Xiancheng; Chugh, Jeetender; Casiano-Negroni, Anette et al. (2014) Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 426:3201-3213 |
| Vashisth, Harish; Skiniotis, Georgios; Brooks 3rd, Charles Lee (2014) Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 114:3353-65 |
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