Thermochemistry of 1-Methylnaphthalene Hydroconversion: Comparison of Group Contribution and ab Initio Models

2013 ◽  
Vol 27 (9) ◽  
pp. 5475-5482
Author(s):  
Maria S. Contreras ◽  
Theodorus de Bruin ◽  
Pascal Mougin ◽  
Hervé Toulhoat
Keyword(s):  
Ab Initio ◽  
Group Contribution ◽  
Ab Initio Models

scholarly journals A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

2021 ◽  
Vol 26 (2) ◽  
pp. 39
Author(s):  
Juan P. Sánchez-Hernández ◽  
Juan Frausto-Solís ◽  
Juan J. González-Barbosa ◽  
Diego A. Soto-Monterrubio ◽  
Fanny G. Maldonado-Nava ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Primary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Golden Ratio ◽  
Small Peptides ◽  
Hybrid Simulated Annealing ◽  
Ab Initio Models

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.

scholarly journals Combining unconventional MR with AMPLE ab initio models and experimental phasing

2016 ◽  
Vol 72 (a1) ◽  
pp. s200-s200
Author(s):  
Adam J. Simpkin ◽  
Olga Mayans ◽  
Daniel J. Rigden ◽  
Martin Savko ◽  
William E. Shepard ◽  
...  
Keyword(s):  
Ab Initio ◽  
Experimental Phasing ◽  
Ab Initio Models

Ab Initio Group Contribution Method for Activation Energies of Hydrogen Abstraction Reactions

ChemPhysChem ◽  
2006 ◽  
Vol 7 (1) ◽  
pp. 188-199 ◽  
Author(s):  
Mark Saeys ◽  
Marie-Françoise Reyniers ◽  
Veronique Van Speybroeck ◽  
Michel Waroquier ◽  
Guy B. Marin
Keyword(s):  
Ab Initio ◽  
Hydrogen Abstraction ◽  
Activation Energies ◽  
Group Contribution ◽  
Group Contribution Method

Ab initio models for metalation and hydrogenolysis reactions involving organolithium compounds

1989 ◽  
Vol 111 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Elmar Kaufmann ◽  
Stefan Sieber ◽  
Paul v. R. Schleyer
Keyword(s):  
Ab Initio ◽  
Organolithium Compounds ◽  
Ab Initio Models

Ab initio group contribution method for activation energies for radical additions

AIChE Journal ◽  
2004 ◽  
Vol 50 (2) ◽  
pp. 426-444 ◽  
Author(s):  
Mark Saeys ◽  
Marie-Fran�oise Reyniers ◽  
Guy B. Marin ◽  
Veronique Van Speybroeck ◽  
Michel Waroquier
Keyword(s):  
Ab Initio ◽  
Activation Energies ◽  
Group Contribution ◽  
Group Contribution Method
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