The overall goal of this proposed Research Resource is the development and integration of modeling tools for the exploration of multiresolution models in structural biology. Today's important 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 will be focused on the development of new and integrated approaches to multiscale modeling in three primary focus areas: Modeling of large-scale assemblies of nucleic acids and proteins with nucleic acids, including the facile construction of models at full atomic resolution and the incorporation of low resolution information regarding structure into mechanically based empirical potentials. New Methods that combine lattice based dynamic Monte Carlo and all atom molecular dynamics (MD) will be developed to address critical sampling and timescale issues in molecular simulations of protein and peptide folding. Virus assembly, which will include the extension of finite difference methods for Poisson-Boltzmann calculations to symmetry-adapted solutions, thereby reducing the computational costs associated with studies of large symmetric assemblies, and the development and exploration of reduced representation (shape based) models for virus assembly. An additional core research effort that ties these threads together will be the development and distribution of computer codes to make such simulations readily accessible to the scientific community at large. The result of these developments will be new computer codes to provide a more integrated approach to multiscale modeling of proteins, nucleic acids and their complexes and assemblies. We will complement these developments by: Dissemination and distribution of our algorithmic and methodological developments through the well established distribution mechanisms employed for the widely distributed AMBER and CHARMM molecular modeling packages, and 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 |
| Montiel-García, Daniel J; Mannige, Ranjan V; Reddy, Vijay S et al. (2016) Structure based sequence analysis of viral and cellular protein assemblies. J Struct Biol 196:299-308 |
| 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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