## High Level, Long Term Vision

+ Identify Structure/Function Relationships

  - Determine active sites and "mates" on unknown structures. Find
    ligand binding sites and potential protein/protein interactions. 

  - Determine how changes to structure might induce changes to
    function. (e.g. find hotspots for mutation)

  - Determine the geometric, kinematic, and dynamic mechanisms for
    chemical processes.

## Ideas on Achieving these goals

+ Determination of "features" for performing matching and
  categorization. Various tasks on the top list would be addressed
  this way (active site function determination, hotspot finding, ...) 

  - features that categorize geometry / spatial chemistry, not
    necessarily underlying sequence

  - features that are "stable" across the diversity of similar
    functions and motions

+ Applying good "informatics" techniques to these "features"

  - bag of feature methods
  - flexible templates

+ Simplified representations of geometric complexity and motions

+ "Molecular Morphing" as a useful tool - especially when things can
  be "driven" and stay "feasible"

  - drive molecules between different configurations to perform
    comparisons

  - "pry open" closed things, "pull closed" open things to get ideas
    of what they look like in different states

## Core technical components

+ Good "kinematic simulation" of molecules to move between different
  states, or make two dissimilar things similar enough to look at.

  - elastic normal modes + direction projection, differential
    disallowment, re-rigidification (FRODA-style)

  - differential disallowment advantages:
    - can do stabilization
    - can be "driven" towards goals more easily
    - can be tuned (but needs to be tuned)
    - can deal with non-overlap constraints
    - can use hierarchical methods (for both collisions and for
      movement) 

+ Geometric feature points

  - Finite things to try to match / accumulate / ...
  - Stability across diversity
  - independent of representation

## Visualization tasks

+ Be able to compare interfaces (across different molecules, same
  molecule in different states, ...)

  - determine stability of properties of interest

+ Look at motions - understand what's the same and different