a score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness得分能力的蛋白质三维模型检索自己的序列作为一个定量测量的质量和适当性.pdfVIP

A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness ´ ´ 1,2 ´ 1 Leon P. Martınez-Castilla , Rogelio Rodrıguez-Sotres * ´ ´ ´ ´ ´ 1 Departamento de Bioquımica–Facultad de Quımica, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Distrito Federal, Mexico, 2 Centro de Ciencias de la ´ ´ ´ Complejidad, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Distrito Federal, Mexico Abstract Background: Despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three- dimensional fold, and in turn determines its function remains an elusive question. Alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. However, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. Folding pattern diversity seems to be much narrower than sequence diversity, and the amino acid sequences of natural proteins have evolved under a selective pressure comprising structural and functional requirements acting in parallel. Principal Findings: The approach described in this work begins by generating a large number of amino acid sequences using ROSETTA [Dantas G et al. (2003) J Mol Biol 332:449–460], a program with notable robustness in the assignment of amino acids to a known three-dimensional structure. The resulting sequence-sets showed no conservation of amino acids at active sites, or protein-protein interface