title: CplexA: a Mathematica package to study macromolecular-assembly control of gene expression.
abstract: CONCLUSIONS
  Macromolecular assembly coordinates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors.
  
  
  BACKGROUND
  CplexA is freely available together with documentation at http://sourceforge.net/projects/cplexa/.
authors.affiliation: Biophysics Unit (CSIC-UPV/EHU), University of the Basque Country, Bilbao, Spain. j.vilar@ikerbasque.org
authors.forename: Jose M G
authors.initials: JM
authors.lastname: Vilar
authors.forename: Leonor
authors.initials: L
authors.lastname: Saiz
mesh_terms: D015870:Gene Expression; D005786:Gene Expression Regulation; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors