Protein Linear Indices in Bioinformatics Studies: 1. Prediction of Protein Stability Effects of a Complete Set of Alanine Substitutions in Arc Repressor

2006 ◽  
Author(s):  
Juan Castillo-Garit ◽  
Yovani Marrero-Ponce ◽  
Ricardo Medina-Marrero ◽  
Vicente Romero-Zaldivar ◽  
Francisco Torrens ◽  
...  
Keyword(s):  
Protein Stability ◽  
Complete Set ◽  
Arc Repressor

Protein linear indices of the ‘macromolecular pseudograph α-carbon atom adjacency matrix’ in bioinformatics. Part 1: Prediction of protein stability effects of a complete set of alanine substitutions in Arc repressor

2005 ◽  
Vol 13 (8) ◽  
pp. 3003-3015 ◽  
Author(s):  
Yovani Marrero-Ponce ◽  
Ricardo Medina-Marrero ◽  
Juan A. Castillo-Garit ◽  
Vicente Romero-Zaldivar ◽  
Francisco Torrens ◽  
...  
Keyword(s):  
Carbon Atom ◽  
Protein Stability ◽  
Adjacency Matrix ◽  
Complete Set ◽  
Arc Repressor

scholarly journals tomocomd-camps and protein bilinear indices - novel bio-macromolecular descriptors for protein research: I. Predicting protein stability effects of a complete set of alanine substitutions in the Arc repressor

FEBS Journal ◽  
2010 ◽  
Vol 277 (15) ◽  
pp. 3118-3146 ◽  
Author(s):  
Sadiel E. Ortega-Broche ◽  
Yovani Marrero-Ponce ◽  
Yunaimy E. Díaz ◽  
Francisco Torrens ◽  
Facundo Pérez-Giménez
Keyword(s):  
Protein Stability ◽  
Protein Research ◽  
Complete Set ◽  
Arc Repressor

Protein stability effects of a complete set of alanine substitutions in Arc repressor

1994 ◽  
Vol 1 (8) ◽  
pp. 518-523 ◽  
Author(s):  
Marcos E. Milla ◽  
Bronwen M. Brown ◽  
Robert T. Sauer
Keyword(s):  
Protein Stability ◽  
Complete Set ◽  
Arc Repressor

Markovian Backbone Negentropies: Molecular descriptors for protein research. I. Predicting protein stability in Arc repressor mutants

2004 ◽  
Vol 56 (4) ◽  
pp. 715-723 ◽  
Author(s):  
Ronal Ramos de Armas ◽  
Humberto González Díaz ◽  
Reinaldo Molina ◽  
Eugenio Uriarte
Keyword(s):  
Protein Stability ◽  
Molecular Descriptors ◽  
Protein Research ◽  
Arc Repressor

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

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