16 papers · ranked by Valyu relevance
Ban Chen, Shuangshuang Liu, Huiyin Xia, Xican Li + 2 more
'Alan Talevi'] Chinese materia medica (CMM) refers to the medicinal substances used in traditional Chinese medicine. In recent years, CMM has become globally prevalent, and scientific research on CMM has increasingly garnered attention. Computer-aided drug design (CADD) has been employed in Western medicine research…
Megan L. O’Mara, Sarah Rauscher, Stacey D. Wetmore
Megan O’Mara, Sarah Rauscher and Stacey Wetmore introduce the RSC Advances themed collection on New insights into biomolecular systems from large-scale simulations.
Małgorzta Borówko
Rapid advances are taking place in the application of molecular simulations to study complex systems. Molecular simulations are widely used in physics, chemistry, biology, material science, engineering, and even medicine. Each study conducted in a purely theoretical manner can be treated as a simulation. The behavior…
Maya Topf, Edina Rosta, Gregory R. Bowman, Massimiliano Bonomi
Understanding the molecular mechanisms used by biological systems to perform their functions is often essential to rationally target associated diseases. In many cases, the determination of the three-dimensional structure of these systems provides precious insights. However, it is more often the interplay between…
Małgorzata Borówko
Molecular simulation and modeling have a huge and growing impact on scientific progress. We are witnessing a kind of “transfer of experience to cyberspace moving”. This became possible thanks to the development of advanced theories, new computational methods, and, above all, thanks to the unimaginable increase in the…
Marco Tutone, Anna Maria Almerico
Science is a point of view. Two centuries ago, Auguste Comte stated in 1830, “Any attempt to use mathematical methods in the study of chemical problems must be considered profoundly irrational and contrary to the spirit of chemistry…”. But just a few years later (1888), Gay-Lussac changed this perspective: “…perhaps we…
Sonja Mathias, Adrien Coulier, Andreas Hellander
Background Cell-based models are becoming increasingly popular for applications in developmental biology. However, the impact of numerical choices on the accuracy and efficiency of the simulation of these models is rarely meticulously tested. Without concrete studies to differentiate between solid model conclusions and…
Marco Tutone, Anna Maria Almerico
To date, computational approaches have been recognized as a key component in drug design and discovery workflows. Developed to help researchers save time and reduce costs, several computational tools have been developed and implemented in the last twenty years. At present, they are routinely used to identify a…
Ambrish Kumar Srivastava, Konda Reddy Karnati, Kshatresh Dutta Dubey
Computational methods have become powerful enough to describe the biomolecular structures and their interactions. A variety of methods have been developed and implemented successfully to study biomolecular systems and processes up to a certain level of accuracy. For instance, biomolecular processes are mediated by…
Georgia Dorahy, Jake Zheng Chen, Thomas Balle, Lee Wei Lim + 1 more
'Luca Aquili'] Central nervous system (CNS) disorders are a therapeutic area in drug discovery where demand for new treatments greatly exceeds approved treatment options. This is complicated by the high failure rate in late-stage clinical trials, resulting in exorbitant costs associated with bringing new CNS drugs to…
Siddharth Sinha, Benjamin Tam, San Ming Wang, Hugo A. L. Filipe
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction…
Clara Blanes-Mira, Pilar Fernández-Aguado, Jorge de Andrés-López, Asia Fernández-Carvajal + 5 more
'Asia Fernández-Carvajal' 'Antonio Ferrer-Montiel' 'Gregorio Fernández-Ballester' 'Huiyong Sun' 'Peichen Pan' 'Jingyu Zhu'] The rapid advances of 3D techniques for the structural determination of proteins and the development of numerous computational methods and strategies have led to identifying highly active…
Basheer Qolomany, Tristan J. Calay, Liaquat Hossain, Aos Mulahuwaish + 4 more
Cyber competitions are usually team activities, where team performance not only depends on the members’ abilities but also on team collaboration. This seems intuitive, especially given that team formation is a well-studied discipline in competitive sports and project management, but unfortunately, team performance and…
Jaroslaw Krzywanski, Marcin Sosnowski, Karolina Grabowska, Anna Zylka + 3 more
'Anna Zylka' 'Lukasz Lasek' 'Agnieszka Kijo-Kleczkowska' 'Bongju Kim'] This paper provides a comprehensive review of recent advancements in computational methods for modeling, simulation, and optimization of complex systems in materials engineering, mechanical engineering, and energy systems. We identified key trends…
Hang Phuong Nguyen, Hyun-Joo Lee, Sungmin Kim
Purpose In this study, we proposed establishing an automatic computer-assisted surgical planning approach based on average population models. Methods We built the average population models from humerus datasets using the Advanced Normalization Toolkits (ANTs) and Shapeworks. Experiments include (1) evaluation of the…
Bao Tuan Chau, Yuma Miyai, Thomas D Roper
of Bayesian Optimization Utilizing Continuous Chemistry Digital Twins Authors: Bao Tuan Chau, Yuma Miyai, Thomas D Roper A novel chemistry optimization methodology has been developed and applied to digital twins for a nucleophilic aromatic substitution reaction and a two-step process to produce an intermediate for the…