title: RaTrav: a tool for calculating mean first-passage times on biochemical networks.
abstract: BACKGROUND
  The concept of mean first-passage times (MFPTs) occupies an important place in the theory of stochastic processes, with the methods of their calculation being equally important in theoretical physics, chemistry and biology. We present here a software tool designed to support computational biology studies where Markovian dynamics takes place and MFPTs between initial and single or multiple final states in network-like systems are used. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method.
  
  
  RESULTS
  After a brief introduction to RaTrav, we highlight the utility of MFPT calculations by providing two examples (accompanied by Additional file 1) where they are deemed to be of importance: analysis of a protein-protein docking funnel and interpretation of the free energy transduction between two coupled enzymatic reactions controlled by the dynamics of transition between enzyme conformational states.
  
  
  CONCLUSIONS
  RaTrav is a versatile and easy to use software tool for calculating MFPTs across biochemical networks. The user simply prepares a text file with the structure of a given network, along with some additional basic parameters such as transition probabilities, waiting probabilities (if any) and local times (weights of edges), which define explicitly the stochastic dynamics on the network. The RaTrav tool can then be applied in order to compute desired MFPTs. For the provided examples, we were able to find the favourable binding path within a protein-protein docking funnel and to calculate the degree of coupling for two chemical reactions catalysed simultaneously by the same protein enzyme. However, the list of possible applications is much wider.
authors.affiliation: Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK. Paul.Bates@cancer.org.uk.
authors.forename: Mieczyslaw
authors.initials: M
authors.lastname: Torchala
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Chelminiak
authors.forename: Michal
authors.initials: M
authors.lastname: Kurzynski
authors.forename: Paul A
authors.initials: PA
authors.lastname: Bates
mesh_terms: D019295:Computational Biology; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D008390:Markov Chains; D053858:Metabolic Networks and Pathways; D009010:Monte Carlo Method; D011485:Protein Binding; D011487:Protein Conformation; D012984:Software; D013816:Thermodynamics
chemical_list: D004798:Enzymes