Machine Learning In Biomolecular Simulations

Machine learning methods such as neural networks, non-linear dimensionality reduction techniques, random forests and others meet in this research topic with biomolecular simulations. The authors of eight articles applied these methods to analyze simulation results, accelerate simulations or to make molecular mechanics force fields more accurate.

Dr. Sergio Decherchi and Dr. Andrea Cavalli are co-founders of BiKi Technologies s.r.l. - a company that commercializes a Molecular Dynamics-based software suite for drug discovery. All other Topic Editors declare no competing interests with regards to the Research Topic subject.

A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.

This book elucidates the sustainable production of commercially important biomolecules in medicines, food, and beverage processing, through biological systems, including microorganisms, animal cells, plant cells, tissues, enzymes, and in vitro. It discusses promising technologies for the manipulation of cells including, genetic engineering, synthetic biology, genome editing, and metabolic engineering. The initial chapters of the book introduce topics on biomanufacturing, circular economy, strain design and improvement, upstream and downstream processing. The subsequent chapters cover artificial intelligence-assisted production, designer cell factories, biosensors for monitoring biomolecules, different cells factories, biosynthetic pathways, and genome editing approaches for scale-up biomanufacturing. Lastly, the book discusses the opportunities and challenges of implementing biological systems for the production of biomolecules. ​This book is a valuable source for students, researchers, scientists, clinicians, stakeholders, policymakers, and practitioners to understand biomanufacturing for the sustainable production of biomolecules.

Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. Presents computational theory alongside case studies to help readers understand the use of simulation in practice Includes extensive examples of different types of simulation methods and approaches to result analysis Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems

This textbook provides an introduction to the fundamental and applied aspects of biophysics for advanced undergraduate and graduate students of physics, chemistry, and biology. The application of physics principles and techniques in exploring biological systems has long been a tradition in scientific research. Biological systems hold naturally inbuilt physical principles and processes which are popularly explored. Systematic discoveries help us understand the structures and functions of individual biomolecules, biomolecular systems, cells, organelles, tissues, and even the physiological systems of animals and plants. Utilizing a physics- based scientific understanding of biological systems to explore disease is at the forefront of applied scientific research. This textbook covers key breakthroughs in biophysics whilst looking ahead to future horizons and directions of research. It contains models based on both classical and quantum mechanical treatments of biological systems. It explores diseases related to physical alterations in biomolecular structures and organizations alongside drug discovery strategies. It also discusses the cutting- edge applications of nanotechnologies in manipulating nanoprocesses in biological systems. Key Features: • Presents an accessible introduction to how physics principles and techniques can be used to understand biological and biochemical systems. • Addresses natural processes, mutations, and their purposeful manipulation. • Lays the groundwork for vitally important natural scientific, technological, and medical advances. Mohammad Ashrafuzzaman, a biophysicist and condensed matter scientist, is passionate about investigating biological and biochemical processes utilizing physics principles and techniques. He is a professor of biophysics at King Saud University’s Biochemistry Department in the College of Science, Riyadh, Saudi Arabia; the co- founder of MDT Canada Inc., and the founder of Child Life Development Institute, Edmonton, Canada. He has authored Biophysics and Nanotechnology of Ion Channels, Nanoscale Biophysics of the Cell, and Membrane Biophysics. He has also published about 50 peer- reviewed articles and several patents, edited two books, and has been serving on the editorial boards of Elsevier and Bentham Science journals. Dr. Ashrafuzzaman has held research and academic ranks at Bangladesh University of Engineering & Technology, University of Neuchatel (Switzerland), Helsinki University of Technology (Finland), Weill Medical College of Cornell University (USA), and University of Alberta (Canada). During 2013– 2018 he also served as a Visiting Professor at the Departments of Oncology, and Medical Microbiology and Immunology, of the University of Alberta. Dr. Ashrafuzzaman earned his highest academic degree, Doctor of Science (D.Sc.) in condensed matter physics from the University of Neuchatel, Switzerland in 2004.

Handbook of Biomolecules: Fundamentals, Properties and Applications is a comprehensive resource covering new developments in biomolecules and biomaterials and their industrial applications in the fields of bioengineering, biomedical engineering, biotechnology, biochemistry, and their detection methods using biosensors. This book covers the fundamentals of biomolecules, their roll in living organism, structure, sources, important characteristics, and the industrial applications of these biomaterials. Sections explore amino acids, carbohydrates, nucleic acids, proteins, lipids, metabolites and natural products, then go on to discuss purification techniques and detection methods. Applications in biomolecular engineering, biochemistry and biomedical engineering, among others, are discussed before concluding with coverage of biomolecules as anticorrosion materials. Provides the chronological advancement of biomolecules, their biochemical reaction, and many modern industrial applications in engineering and science Serves as a valuable source for researchers interested in the fundamentals, basics and modern applications of biomolecules Covers both synthetic and natural biomolecule synthesis and purification processes and their modern applications Bridges the gap between the fundamental science of biomolecular chemistry and the relevant technology and industrial applications

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.