title: MTBindingSim: simulate protein binding to microtubules.
abstract: CONCLUSIONS
  Many protein-protein interactions are more complex than can be accounted for by 1:1 binding models. However, biochemists have few tools available to help them recognize and predict the behaviors of these more complicated systems, making it difficult to design experiments that distinguish between possible binding models. MTBindingSim provides researchers with an environment in which they can rapidly compare different models of binding for a given scenario. It is written specifically with microtubule polymers in mind, but many of its models apply equally well to any polymer or any protein-protein interaction. MTBindingSim can thus both help in training intuition about binding models and with experimental design.
  
  
  METHODS
  MTBindingSim is implemented in MATLAB and runs either within MATLAB (on Windows, Mac or Linux) or as a binary without MATLAB (on Windows or Mac). The source code (licensed under the GNU General Public License) and binaries are freely available at http://mtbindingsim.googlecode.com.
  
  
  BACKGROUND
  jphilip@nd.edu; cpence@nd.edu.
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. jphilip@nd.edu
authors.forename: Julia T
authors.initials: JT
authors.lastname: Philip
authors.forename: Charles H
authors.initials: CH
authors.lastname: Pence
authors.forename: Holly V
authors.initials: HV
authors.lastname: Goodson
mesh_terms: D019295:Computational Biology; D007700:Kinetics; D008870:Microtubules / Q000378:metabolism; D008954:Models, Biological; D011381:Programming Languages; D011485:Protein Binding; D012984:Software