This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Yammp is a general purpose molecular mechanics program, initially developed for coarse-grain modeling of macromolecular systems, although we have tackled some all-atom problems with Yammp. It was originally applied to a range of unrelated problems (DNA supercoiling, the structure of the ribosome, and mean-field simulations on model membranes, among others). As demand for coarse-grained models grew, we decided to rewrite Yammp into a form (Yammp2) that would enable it to become an extension of Python. The result is YUP (Yammp Under Python), which has additional data types that are particularly useful for molecular mechanics calculations. YUP (Yammp Under Python) is an extension of Python, with additional data types that are particularly useful for molecular mechanics calculations. YUP is therefore highly programmable, which is its main strength. The user will find, however, that YUP requires more effort to learn than does a traditional molecular mechanics program, where one can build models and run simulations quickly, either from a GUI, or by modifying other people s scripts. In order to use YUP, one needs to commit to becoming a YUP programmer.
| 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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