Molecules 2004, 9(12), 1124-1147; doi:10.3390/91201124
Article

Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability

1,* email, 3, 4, 2, 2, 5 and 6
Received: 2 June 2004; in revised form: 12 December 2004 / Accepted: 13 December 2004 / Published: 31 December 2004
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract: This report describes a new set of macromolecular descriptors of relevance toprotein QSAR/QSPR studies, protein’s quadratic indices. These descriptors are calculatedfrom the macromolecular pseudograph’s α-carbon atom adjacency matrix. A study of theprotein stability effects for a complete set of alanine substitutions in Arc repressorillustrates this approach. Quantitative Structure-Stability Relationship (QSSR) modelsallow discriminating between near wild-type stability and reduced-stability A-mutants. Alinear discriminant function gives rise to excellent discrimination between 85.4% (35/41)and 91.67% (11/12) of near wild-type stability/reduced stability mutants in training andtest series, respectively. The model’s overall predictability oscillates from 80.49 until82.93, when n varies from 2 to 10 in leave-n-out cross validation procedures. This valuestabilizes around 80.49% when n was
Keywords: Protein Stability; Arc Repressor; Alanine-Substitution Mutant; TOMOCOMD Software; Protein Quadratic Indices; QSPR.
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MDPI and ACS Style

Ponce, Y.M.; Marrero, R.M.; Castro, E.A.; Ramos de Armas, R.; Díaz, H.; Zaldivar, V.R.; Torrens, F. Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability. Molecules 2004, 9, 1124-1147.

AMA Style

Ponce YM, Marrero RM, Castro EA, Ramos de Armas R, Díaz H, Zaldivar VR, Torrens F. Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability. Molecules. 2004; 9(12):1124-1147.

Chicago/Turabian Style

Ponce, Yovani M.; Marrero, Ricardo M.; Castro, Eduardo A.; Ramos de Armas, Ronal; Díaz, Humberto González; Zaldivar, Vicente R.; Torrens, Francisco. 2004. "Protein Quadratic Indices of the “Macromolecular Pseudograph’s α-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability." Molecules 9, no. 12: 1124-1147.

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