Research projects under the MMTSB Core are guided, extended and complemented by our ongoing Collaborative Research Efforts. Throughout the course of our resource activities collaborative projects finish and new ones are initiated. Scientists interested in becoming involved in collaborative projects with MMTSB scientists are encouraged to contact an MMTSB Center investigator.

Current collaborative projects include:

  • Modeling ribosomal particles from E. coli with Joachim Frank. This will focus our development efforts in this area on important experimental systems and provide the opportunity for input on software development from a key player in nucleic acid structure and function. Dr Frank has collaborated with two of our resource scientists in the past and his continued involvement will help us keep abreast of the most timely issues in modeling these large composite particles (Projects IV and V).
  • Investigations of the assembly dynamics and energetics of ribosomal particles and RNA through collaborative efforts with Jamie Williamson, Andy McCammon and Joachim Frank. These collaborative investigators bring extensive experience in exploring the assembly of the 30S ribosomal particle and issues of RNA folding, RNA secondary structure formation, molecular electrostatic interactions in large molecular assemblies and ribosome structure and functional dynamics, respectively. These collaborative projects will interface with Projects I and IV.
  • Investigation of the structure and dynamics of eukaryotic chromosomes in vivo, in collaboration with Job Dekker of the University of Massachusetts. Dekker's laboratory has developed chemical cross-linking methods that reveal the relative contact frequencies of different regions of the chromosome. Their initial data were consistent with an analytical model that treated the entire chromosome as an elastic polymer with a uniform persistence length, but more extensive data have revealed regions of different flexibilities, requiring more complex computational models.
  • Additional focus on model building, refinement and functional rearrangement of large systems associated with biologically important macromolecular assemblies (myosin, anthrax, chaperons (GroEL), large enzymes (gutamate dehydrogenase), and the phi29 connector associated with DNA packaging) will be provided through our collaborations with Ken Taylor, Alok Mitra, Mark Fisher and Ed Gogol, Tom Smith and Jiali Gao, respectively. Each of these scientists is a leading expert in the structure and function of the molecular assemblies noted and their involvement as collaborators will significantly assist our refinement of the tools developed in Projects IV and V.
  • Extending the range of approaches used to explore virus assembly and the continued exploration of the mechanical properties of virus capsids will be achieved through collaborative efforts with Adam Zlotnick, Robijn Bruinsma and Rob Phillips. Collaborative projects with this group of scientists will assist our Core efforts in the development of simple physical models for the assembly of virus capsids and the structural and mechanical properties of assembled virus particles (Project III).
  • Establishing new and strong links between MMTSB and the Research Collaboratory for Structural Bioinformatics (RCSB/PDB) in the area of virus structure and analysis will be a key emphasis. In a collaborative effort with Helen Berman, MMTSB and the VIPER web-base will become an integrated component of the PDB.
  • Explorations of RNA packaging in virus capsids using multi-resolution RNA models will be driven by collaborative efforts between two resource PIs (Johnson and Harvey) through Core Projects I, III and independent funding recently acquired by RR PI to investigate DNA and RNA packaging (Harvey).
  • Advances in visualization of virus particles and their constituent molecular components will enhance our continued development of the VIPER web-base and be afforded through collaborative efforts with Chandrajit Bajaj from Center for Computational Visualization, University of Texas, Austin, Texas. Additionally, interactions with Manjunath Kini will explore protein-protein interactions within virus capsids. These collaborations will strengthen the software integration core (Project V) as well as our dissemination and web presence for the VIPER site.
  • Furthering the interdigitation between the Core Projects, collaborative efforts with Shuang Huang will explore emerging bioinformatics regarding virus sequence/structure/assembly relationships and structural modeling associated with the engineering of surface epitope loops to explore the display of the antigenic epitopes to prime the immune system against the known pathogens and toxins. This collaborative component will interface with Projects II and III.
  • Extending the functionality of our structure and modeling tools and structure prediction infrastructure through collaborations with former MMTSB scientist Michael Feig and with the developer and project leader of the BOINC team at Berkeley, David Anderson. The Feig collaboration will focus on extension of the MMTSB Tool Set to include enhanced functionality for nucleic acids as well as implementation of a molecular dynamics repository and analysis facility. Work with the BOINC (Berkeley Open Infrastructure for Network Computing) team will strengthen the structure prediction infrastructure utilized recently in CASP6, and its further development as part of our structure prediction and multi-scale sampling Core Project (II).
  • Exploit recent MMTSB RR developments in the areas of solvation models, including implicit solvent/implicit membrane generalized Born models, and advanced sampling methods, like the replica-exchange molecular dynamics methods integrated into the MMTSB Tool Set, to address key issues in the de novo structure determination of proteins in solution and membrane protein insertion and folding, through collaborations with Jane Dyson and Steve White, and in partially (or fully) ordered environments with Stanley Opella, the directory of the NIBIB Center for NMR Spectroscopy and Imaging of Proteins. Through these collaborations we will harden the methods and models developed as components of Projects I and II.

  • Develop new and perptuate existing collaborative efforts to organize training and research workshops with neighboring centers including the CTBP directed by Jose' Onuchic, NRAMM overseen by Bridget Carragher and Clint Potter and the Pittsburgh Super Computing Center.