A Hybrid Evolutionary Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice Model

2017 ◽  
pp. 628-638 ◽  
Author(s):  
Daniel Varela ◽  
José Santos
Keyword(s):  
Protein Structure ◽  
Evolutionary Algorithm ◽  
Protein Structure Prediction ◽  
Lattice Model ◽  
Structure Prediction ◽  
Face Centered Cubic ◽  
Cubic Lattice ◽  
Hybrid Evolutionary Algorithm ◽  
The Face ◽  
Face Centered

scholarly journals How Good Are Simplified Models for Protein Structure Prediction?

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Swakkhar Shatabda ◽  
M. A. Hakim Newton ◽  
Mahmood A. Rashid ◽  
Duc Nghia Pham ◽  
Abdul Sattar
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Search Algorithm ◽  
Protein Chain ◽  
Face Centered Cubic ◽  
Energy Functions ◽  
Energy Models ◽  
Discrete Lattices ◽  
Face Centered

Protein structure prediction (PSP) has been one of the most challenging problems in computational biology for several decades. The challenge is largely due to the complexity of the all-atomic details and the unknown nature of the energy function. Researchers have therefore used simplified energy models that consider interaction potentials only between the amino acid monomers in contact on discrete lattices. The restricted nature of the lattices and the energy models poses a twofold concern regarding the assessment of the models. Can a native or a very close structure be obtained when structures are mapped to lattices? Can the contact based energy models on discrete lattices guide the search towards the native structures? In this paper, we use the protein chain lattice fitting (PCLF) problem to address the first concern; we developed a constraint-based local search algorithm for the PCLF problem for cubic and face-centered cubic lattices and found very close lattice fits for the native structures. For the second concern, we use a number of techniques to sample the conformation space and find correlations between energy functions and root mean square deviation (RMSD) distance of the lattice-based structures with the native structures. Our analysis reveals weakness of several contact based energy models used that are popular in PSP.

Antiferromagnetism in the Face-Centered Cubic Lattice. II. Magnetic Properties of MnO

1965 ◽  
Vol 139 (4A) ◽  
pp. A1313-A1327 ◽  
Author(s):  
M. E. Lines ◽  
E. D. Jones
Keyword(s):  
Magnetic Properties ◽  
Face Centered Cubic ◽  
Cubic Lattice ◽  
The Face ◽  
Face Centered

MINIMAL KNOTTING NUMBERS

2009 ◽  
Vol 18 (08) ◽  
pp. 1159-1173 ◽  
Author(s):  
CASEY MANN ◽  
JENNIFER MCLOUD-MANN ◽  
RAMONA RANALLI ◽  
NATHAN SMITH ◽  
BENJAMIN MCCARTY
Keyword(s):  
The Body ◽  
Computer Algorithm ◽  
Face Centered Cubic ◽  
Body Centered Cubic ◽  
Cubic Lattice ◽  
The Face ◽  
Face Centered ◽  
Body Centered Cubic Lattice

This article concerns the minimal knotting number for several types of lattices, including the face-centered cubic lattice (fcc), two variations of the body-centered cubic lattice (bcc-14 and bcc-8), and simple-hexagonal lattices (sh). We find, through the use of a computer algorithm, that the minimal knotting number in sh is 20, in fcc is 15, in bcc-14 is 13, and bcc-8 is 18.

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