Comparison Of HSRNAFold and RNAFold Algorithms for RNA Secondary Structure Prediction.

Ribonucleic Acid (RNA) has important structural and functional roles in the cell and plays roles in many stages of protein synthesis. The structure of RNA largely determines its function

Adaptive And Cooperative Harmony Search Models For Rna Secondary Structure Prediction

Penentuan fungsi molekul RNA amat bergantung kepada struktur sekunderya. Kaedah fizikal yang sedia ada untuk penentuan struktur sekunder adalah mahal dan memakan masa. Determining the function of RNA molecules relies heavily on its secondary structure

Adaptive and cooperative harmony search models for RNA secondary structure prediction

Penentuan fungsi molekul RNA amat bergantung kepada struktur sekundernya. Kaedah fizikal yang sedia ada untuk penentuan struktur sekunder adalah mahal dan memakan masa. Beberapa algoritma telah dicadangkan untuk peramalan struktur sekunder RNA, termasuk pengaturcaraan dinamik dan algoritma metaheuristik. Determining the function of RNA molecules relies heavily on its secondary structure. The current physical methods for secondary structure determination are expensive and time consuming. Several algorithms have been proposed for the RNA secondary structure prediction, including dynamic programming and metaheuristic algorithms

Analysis of protein thermostability enhancing factors in industrially important thermus bacteria species

Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the largest negative minimum folding energy (MFE) as predicted by the UNAFold algorithm, were statistically analyzed. Favored substitutions of amino acids residues and their properties were determined. Substitutions were analyzed in modeled protein structures to determine their locations and contribution to energy differences using PyMOL and FoldX programs respectively. Dominant trends in amino acid substitutions consistent with differences in thermostability between orthologous sequences were observed. T. thermophilus thermophilic proteins showed an increase in non-polar, tiny, and charged amino acids. An abundance of alanine substituted by serine and threonine, as well as arginine substituted by glutamine and lysine was observed in T. thermophilus HB27. Structural comparison showed that stabilizing mutations occurred on surfaces and loops in protein structures

Advances in Evolutionary Algorithms

With the recent trends towards massive data sets and significant computational power, combined with evolutionary algorithmic advances evolutionary computation is becoming much more relevant to practice. Aim of the book is to present recent improvements, innovative ideas and concepts in a part of a huge EA field

Current Challenges in Modeling Cellular Metabolism

Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results

Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u

The methyltransferase and helicase enzymes as therapeutic targets of Zika virus : a bio- computational analysis of interactions with potential inhibitors.

Doctoral of Philosophy in Pharmaceutical Sciences. University of KwaZulu-Natal, Westville, 2019.The rampant Zika virus has received worldwide attention after becoming a global crisis following the Brazilian epidemic in 2015. From an obscure and neglected pathogen, Zika virus is now a notorious virus associated with neurological disorders in infants and adults. Since 2016, the rapid research response from the global scientific community have led to the discovery of numerous potential small molecule inhibitors and vaccines against the Zika virus. Although, in spite of this massive research initiative, there is still no effective antiviral nor vaccine that has made it out of clinical trials. The design and development of new chemical entities demands excessive cost, time and resources. Therefore, this study applies computer-aided drug design techniques, which accelerates the rational drug design process. Computational approaches including molecular docking, virtual screening, molecular modeling and molecular dynamics facilitate the filtration of large databases of compounds to sift out potential lead compounds. Furthermore, research has dedicated several resources toward FDA-approved drug repurposing. Generally, drugs have similar effects on viruses of the same family; hence drugs that have previously been effective in treating other flaviviruses, such as Dengue virus and West Nile virus, are being tested for its potential inhibition of Zika virus. However, the ability of these drugs to pass the bloodbrain barrier to treat infected neurons poses a challenge to anti-Zika virus drug discovery. This study proposes innovative strategies to design drugs that are capable of passing the blood-brain barrier, and to be able to use drugs that are impermeable via drug delivery mechanisms. This study also assesses the bioavailability and blood-brain barrier permeability of screened drugs to scrutinize the list of potential Zika virus inhibitors. Apart from identifying potential inhibitors, understanding the structural dynamics of viral targets and molecular mechanisms underlying potential inhibition of the virus is imperative. This study explores the structural and molecular dynamics of key targets of the Zika virus, the NS3 helicase and the NS5 methyltransferase enzymes, using computational approaches mentioned above and several others elaborated in this thesis. These computational methods also allowed the identification of precise interactions, amino acid residues, inhibitory mechanisms and pharmacophoric features involved in binding of lead compounds to these enzymes. IX Chapter 4 represents the first study of this thesis, which presents a concise literature background of Zika virus and identifies blood-brain barrier permeability as a core challenge in anti-Zika virus drug development. This study also provides approaches that may enable researchers to create effective anti-Zika virus drugs. Chapter 5 is the subsequent study of this thesis, which applies molecular dynamics to comparatively investigate the mechanism of inhibition and binding mode of two potential inhibitors, sinefungin and compound 5, to the NS5 methyltransferase. The specific pharmacophoric moieties of the most stable inhibitor are also identified in this study. Chapter 6 is the final study of this thesis, which examines the structural dynamics of the Zika virus NS3 helicase enzyme upon binding of ATPase inhibitor and flavivirus lead compound, resveratrol, and reports the key interactions and amino acid residues of the NS3 helicase that contribute highly to binding of resveratrol. This thesis presents an all-inclusive in silico assessment to advance research in drug design and development of Zika virus inhibitors, thus providing a greater understanding of the structural dynamics that occur in unbound and inhibitor-bound Zika virus target enzymes. Therefore, the constituents of this thesis are considered an essential platform in the progression of research toward anti-ZIKV drug design, discovery and delivery against Zika virus