Threading a sequence through a set of structures

Contact capacity potentials reflect mainly hydrophobicity of the amino acids. Hydrophobicity is the major driving force for protein folding. Without pairwise contact potentials we can use a simple and fast dynamic programming algorithm to align a sequence with a structure.

• Thread 1- to 3-D with 123D+

• Paper on 123D (PostScrip format)
• Fold library
• Compare protein structures
• Domain assignment

Reference:

N.N. Alexandrov, R. Nussinov and R.M. Zimmer
Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
Pacific Symposium on Biocomputing '96 (Lawrence Hunter & Teri E. Klein, Eds) 1995, World Scientific Publishing Co., Singapore, pp. 53-72

Links2Go Recognition