A Metaheuristic Approach to Protein Structure Prediction

Abstract

The Emergence, Complexity and Computation (ECC) series publishes new developments, advancements and selected topics in the fields of complexity, computation and emergence. The series focuses on all aspects of reality-based computation approaches from an interdisciplinary point of view especially from applied sciences, biology, physics, or chemistry. It presents new ideas and interdisciplinary insight on the mutual intersection of subareas of computation, complexity and emergence and its impact and limits to any computing based on physical limits (thermodynamic and quantum limits, Bremermann's limit, Seth Lloyd limits…) as well as algorithmic limits (Gödel's proof and its impact on calculation, algorithmic complexity, the Chaitin's Omega number and Kolmogorov complexity, non-traditional calculations like Turing machine process and its consequences,…) and limitations arising in artificial intelligence field. The topics are (but not limited to) membrane computing, DNA computing, immune computing, quantum computing, swarm computing, analogic computing, chaos computing and computing on the edge of chaos, computational aspects of dynamics of complex systems (systems with self-organization, multiagent systems, cellular automata, artificial life,…), emergence of complex systems and its computational aspects, and agent based computation. The main aim of this series it to discuss the above mentioned topics from an interdisciplinary point of view and present new ideas coming from mutual intersection of classical as well as modern methods of computation. Within the scope of the series are monographs, lecture notes, selected contributions from specialized conferences and workshops, special contribution from international experts.

Aplicação de Evolução Diferencial em GPU Para o Problema de Predição de Estrutura de Proteínas com Modelo 3D AB Off-Lattice

“…Dois aminoácidos se conectam para formar uma ligação peptídica. Isso acontece quando o grupo carboxílico de um aminoácido se conecta com o grupo amina de outro [Jana and Sil 2018].…”

“…O método ab initio propõe um modelo matemático que representa a energia livre de possíveis conformações de proteínas a partir da sua cadeia de aminoácidos e suas propriedades físico-químicas. O modelo AB Off-Lattice, considera a propriedade de hidrofobicidade dos aminoácidos de maneira que os aminoácidos hidrofóbicos tendem a ficar no centro das proteínas e os hidrofílicos na parte externa [Jana and Sil 2018]. Nesse modelo o ângulo entre aminoácido adjacentes é considerado.…”

Ab Initio Protein Structure Prediction Using Evolutionary Approach: A Survey

“…The Protein Structure Prediction (PSP) problem is to determine the three-dimensional structure (the native conformation) of a protein given its primary structure, i.e., a sequence of amino acids [3]. Some human disorders caused by protein misfolding include Alzheimer's disease, neurodegenerative diseases and certain types of cancer [4]. Thus, the prediction of the protein structure is a challenge for the area of computational biology [4].…”

“…Some human disorders caused by protein misfolding include Alzheimer's disease, neurodegenerative diseases and certain types of cancer [4]. Thus, the prediction of the protein structure is a challenge for the area of computational biology [4].…”

“…Computational methods for PSP can be separated into three category: homology, threading (or fold recognition), and ab initio (also known as de novo prediction) [4]. In homology modeling there is a comparison of sequence similarity.…”