scholarly journals Estratégia Algorítmica para a Reconstrução e Validação da Estrutura Molecular de Variantes do SARS-CoV-2

2021 ◽  
Author(s):  
Clarice de Souza ◽  
João Bessa ◽  
Rosiane de Freitas ◽  
Micael Oliveira ◽  
Kelson Mota
Keyword(s):  
Branch And Prune

Aspectos matemático-computacionais e físico-químicos envolvidos na reconstrução da estrutura molecular tridimensional de proteínas do SARS-CoV-2 são abordados neste artigo, envolvendo a variante P.1 detectada em pacientes infectados em solo brasileiro, principalmente as do estado do Amazonas. Foi realizado um estudo sobre o impacto teórico da P.1 por intermédio da reconstrução estrutural de proteínas onde a mutagênese foi realizada computacionalmente e com o auxílio da implementação de um algoritmo de enumeração implícita de factibilidade, Branch-and-Prune, cujas soluções foram validadas através do uso do gráfico de Ramachandran. Desta forma, mesmo com a ausência de estruturas cristalográficas caracterizando estas mutações, pôde-se computacionalmente modelar uma estrutura tridimensional onde ao fim realizou-se o alinhamento estrutural com a cristalografia do complexo ACE2-RBD

scholarly journals NMR Protein Structure Calculation and Sphere Intersections

2020 ◽  
Vol 8 (1) ◽  
pp. 89-101
Author(s):  
Carlile Lavor ◽  
Rafael Alves ◽  
Michael Souza ◽  
Luis Aragón José
Keyword(s):  
Protein Structures ◽  
Structure Calculation ◽  
Bp Algorithm ◽  
Main Step ◽  
Combinatorial Method ◽  
Nmr Data ◽  
Sampling Process ◽  
Protein Molecules ◽  
Protein Structure Calculation ◽  
Branch And Prune

AbstractNuclear Magnetic Resonance (NMR) experiments can be used to calculate 3D protein structures and geometric properties of protein molecules allow us to solve the problem iteratively using a combinatorial method, called Branch-and-Prune (BP). The main step of BP algorithm is to intersect three spheres centered at the positions for atoms i − 3, i − 2, i − 1, with radii given by the atomic distances di−3,i, di−2,i, di−1,i, respectively, to obtain the position for atom i. Because of uncertainty in NMR data, some of the distances di−3,i should be represented as interval distances [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}], where {\underline{d}_{i - 3,i}} \le {d_{i - 3,i}} \le {\bar d_{i - 3,i}}. In the literature, an extension of the BP algorithm was proposed to deal with interval distances, where the idea is to sample values from [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}]. We present a new method, based on conformal geometric algebra, to reduce the size of [{\underline{d}_{i - 3,i}},{\bar d_{i - 3,i}}], before the sampling process. We also compare it with another approach proposed in the literature.

scholarly journals The Interval Branch-And-Prune Algorithm for the Protein Structure Determination

2017 ◽  
Vol 112 (3) ◽  
pp. 56a
Author(s):  
Thérèse E. Malliavin ◽  
Bradley Worley ◽  
Benjamin Bardiaux ◽  
Guillaume Bouvier ◽  
Mohamed Machat ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Protein Structure Determination ◽  
Branch And Prune Algorithm ◽  
Branch And Prune

scholarly journals A branch-and-prune method to solve closure equations in dual quaternions

2021 ◽  
Vol 164 ◽  
pp. 104424
Author(s):  
Arya Shabani ◽  
Josep M. Porta ◽  
Federico Thomas
Keyword(s):  
Dual Quaternions ◽  
Branch And Prune

NoC contention analysis using a branch-and-prune algorithm

2014 ◽  
Vol 13 (3s) ◽  
pp. 1-26 ◽  
Author(s):  
Dakshina Dasari ◽  
Borislav Nikoli'c ◽  
Vincent N'elis ◽  
Stefan M. Petters
Keyword(s):  
Branch And Prune Algorithm ◽  
Branch And Prune

scholarly journals A branch and prune algorithm for the computation of generalized aspects of parallel robots

2014 ◽  
Vol 211 ◽  
pp. 34-50 ◽  
Author(s):  
S. Caro ◽  
D. Chablat ◽  
A. Goldsztejn ◽  
D. Ishii ◽  
C. Jermann
Keyword(s):  
Parallel Robots ◽  
Branch And Prune Algorithm ◽  
Branch And Prune
Sign in / Sign up

Export Citation Format

Share Document