title: Exploring protein's optimal HP configurations by self-organizing mapping.
abstract: Self-organizing map (SOM) has been used in protein folding prediction when the HP model is employed. The existing work uses a square-like shape lattice with l = m x n points to represent the optimal compact structure of a sequence of l amino acids. In this paper, a general l'-size sequence of amino acids is self-organized in a two dimensional lattice with l (> l') points. The obtained minimum configuration then has a flexible shape, in contrast to the compact structure limited in the lattice. To fulfil this extension, a new self-organizing map (SOM) technique is proposed to deal with the difficulty of the unsymmetric input and output spaces. New competition rules in the training phase are introduced and a local search method is applied to overcome the multi-mapping phenomena. Several HP benchmark examples with up to 36 amino acids are tested to verify the effectiveness of the proposed approach in this paper.
authors.affiliation: Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing 100080, China. zxs@amt.ac.cn
authors.forename: Xiang-Sun
authors.initials: XS
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Zhong-Wei
authors.initials: ZW
authors.lastname: Zhan
authors.forename: Ling-Yun
authors.initials: LY
authors.lastname: Wu
authors.forename: Luonan
authors.initials: L
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D001185:Artificial Intelligence; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D020539:Sequence Analysis, Protein / Q000379:methods*; D055672:Static Electricity; D013329:Structure-Activity Relationship
chemical_list: D000596:Amino Acids; D011506:Proteins