Modeling Protein Flexibility and Motions

As outlined above, there are a number of distinct communities working on computer (and mathematical) modeling of protein flexibility, rigidity, and folding, or on simplified and abstracted models with potential applications to these problems. This workshop proposes to bring together leading experts as well as current graduate students and post-docs from at least four of these communities: mathematicians working on the rigidity theory for structures (frameworks, panel or molecular structures, tensegrity structures); computational geometers working on motions and paths of linkages, polygons, etc.; material scientists modeling rigidity in large molecular configurations; biochemists modeling protein flexing, binding of molecules on proteins, and rigidity as a tool for predicting protein behaviour. The objective is to bring together members of these communities of researchers together to: (i) summarize the state of the art (as it then exists) for modeling protein flexibility and motions using models such as frameworks, linkages, tensegrity structures, robotics kinematics, etc.; (ii) describe unsolved critical problems about current and potential models (mathematical, computational and biochemical), sorting the potential significance of various problems and potential results; (iii) use some working sessions to explore ways to clarify, resolve or solve these problems and propose priority problems and approaches.

The plenary talks should include several full hour presentations from all four areas, with an emphasis on posing questions, conjectures, and directions for work which are comprehensible to all represented audiences. We would include time and space for all participants to present 'poster session' style descriptions of current work, but limit the number of full presentations to give time for organized and informal working groups. We would propose to have, on site, demonstrations, and access on a demonstration basis, software and simulations relevant to the topics at hand.

The invitation list is, of course, incomplete. We want to make an extra effort to include graduate students and recent graduates who are already working in these areas, or who have indicated an interest in moving into this area. Senior researchers would be encouraged to suggest junior researchers for inclusion.

Relevance and Timeliness

In summer of 1998, Thorpe and collaborators organized a workshop at Traverse City (associated with Michigan State) on Rigidity Theory and Its Applications, with an emphasis on applications to material science (modeling glass) and proteins [1]. Kuhn, Thorpe and Whiteley were speakers, as were a number of the people (mathematicians, physicists and biochemists) indicated below as potential participants. In Summer 2000, Thorpe and Kuhn organized a workshop on Protein Folding and Flexibility at Traverse City, at which other invitees (including Whiteley), were contributors. In September 2000, Whiteley organized a one day workshop at the Fields, followed by a special session at the AMS Sectional meeting that weekend, on rigidity and related discrete geometry. A further group of potential invitees (mathematicians, computational geometers) participated in one or both of these events. In June 2002, the organizers received an NIH grant to study New Algorithms for Protein Flexibility under a special program to build collaborations between mathematicians and biologists. In January 2003, a workshop on computations for protein flexibility will be held at the Belairs Institute (McGill, Barbados), involving a number of the invitees.

As indicated above in the Overview, protein modeling is a 'hot area' connected in important ways to results from the human genome projects as well as important theoretical and medical problems. The recent NSF/NIH competition (USA) and the current CIHR program (Canada) to support short term visits by non-biologists to work with biologists are confirmations that collaborations such as this are understood as a vital step towards progress on important problems.

The potential of models from rigidity theory and computational geometry to give insights on problems of biological structure in general, and proteins in particular, is currently being explored in a number of small and medium projects. The interest is there, and one can anticipate that by summer 2004, new results, and carefully refined versions of core problems will be ready for broader discussion. The organizers' NIH grant includes partial funding for a substantial workshop during 2004 and we are seeking an attractive site and additional support to bring together a full range of people representing these communities.

Confirmed Participants

Schedule

Calgary Schedule

Videos

Web Comptes-Rendus