title: ValFold: Program for the aptamer truncation process.
abstract: DNA or RNA aptamers have gained attention as the next generation antibody-like molecules for medical or diagnostic use. Conventional secondary structure prediction tools for nucleic acids play an important role to truncate or minimize sequence, or introduce limited chemical modifications without compromising or changing its binding affinity to targets in the design of improved aptamers selected by Systematic Evolution of Ligands by EXponential enrichment (SELEX). We describe a novel software package, ValFold, capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. ValFold predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm.
  
  
  BACKGROUND
  The database is available for free at http://code.google.com/p/valfold/
authors: VALWAY Technology Center, NEC Soft, Ltd., 1-18-7, Shinkiba Koto-ku, Tokyo 136-8627, Japan.
authors: Joe
authors: J
authors: Akitomi
authors: Shintaro
authors: S
authors: Kato
authors: Yoshihito
authors: Y
authors: Yoshida
authors: Katsunori
authors: K
authors: Horii
authors: Makio
authors: M
authors: Furuichi
authors: Iwao
authors: I
authors: Waga