Protein sequence-structure scores

Wilson, C. A., J. Kreychman, and M. Gerstein. 2000. Assessing annotation transfer for genomics Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 297 233 49. 

Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997 268 209-25. 

Pair potentials vs contact capacity potentials a) a pair potential attributes an energetic contribution to each pair of amino acids a, and aj that are mapped by a sequence-structure alignment onto locations of the amino acids b and b/ of the protein template structure. The contribution depends on the types of residues a, and aj as well as on geometric features of their locations b/, and b/, such as their distance in space or in sequence. Often, only certain pairs of amino acid residues are scored, such as those that are contacting or close in space. The total energy is computed as the sum of all pair contributions, b) a contact capacity potential rates the energetic contribution of an amino acid a, from the protein target... 

R. Ltithy, A. D. McLachlan, and D. Eisenberg. Secondary structure based profiles use of structure conserving scoring tables in searching protein sequence database for structural similarities. Proteins 70 229-239 (1991). 

Simons K T, C Kooperberg, E Huang and D Baker 1997 Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences Using Simulated Annealing and Bayesian Scoring Functions. Journal of Molecular Biology 268 209-225... 

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