18 Best Books on Biomolecular Modelling

“Modelling of Biomolecular Structures and Mechanisms” Book Review: The book delves into the subject of biomolecular structures and their modelling, covering a range of topics such as nucleic acids and their interactions, proteins, membranes, enzymatic processes, and the pharmacological and medical implications of these subjects. It also includes chapters on specialized subjects like Structure Modeling of the Acetylcholine Receptor Channel and Related Ligand Gated Channels and Continuum-Model Studies of Redox Reactions, Complex Formation, and Electron Transfer: The Paradigm of Cytochrome c and Cytochrome c Peroxidase. Both theoretical and practical aspects of the subject are covered in the book.

“Molecular Dynamics: With Deterministic and Stochastic Numerical Methods (Interdisciplinary Applied Mathematics)” Book Review: The book is aimed at a wide range of readers, particularly mathematics students. It offers an in-depth exploration of the algorithms employed in molecular dynamics simulation, encompassing both deterministic and stochastic numerical methods. The book covers the fundamental principles of Hamiltonian mechanics and stochastic differential equations, as well as various topics, including symplectic numerical methods, handling constraints and rigid bodies, efficient treatment of Langevin dynamics, thermostats for controlling the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method. By equipping learners with new and efficient methods, the book enables them to overcome specific challenges that arise in complex applications. The book also offers detailed chapters on Canonical Distribution, Stochastic Differential Equations and Numerical Methods for Stochastic Molecular Dynamics.

“Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions” Book Review: This book is an informative resource for protein chemists, catering to a diverse readership including researchers, specialists, and students. It covers a detailed analysis of proteins and the latest advancements in powerful techniques applied in biosciences. The book also discusses cutting-edge developments in protein chemistry and structural biology and includes a comprehensive comparison of Quantum mechanic and modelling mechanic methods and their applications. Additionally, it provides an overview of enzymatic halogenases and haloperoxidases, along with computational studies on their mechanism and functions.

“Biophysical Approaches Determining Ligand Binding to Biomolecular Targets” Book Review: This book targets individuals in academia and industry who specialize in biomolecular science, particularly graduate and post-doctoral level biologists and chemists. Its focus is on the most recent advancements in biophysics concerning ligand binding. Additionally, it provides an overview of the current techniques used to identify ligands and how to characterize their binding sites and mechanisms. The book stresses the importance of using various techniques in combination, highlighting the strengths and weaknesses of each. This approach helps learners understand why certain techniques are more appropriate than others and how to best leverage their synergies. The book also explains how complementary techniques can be used together to achieve maximum effectiveness.

“Bioinformatics Research and Applications” Book Review: The book covers a range of topics, including data analysis, machine learning, and computational biology. Bourgeois and Wan’s writing is clear and concise, making even the most complex concepts accessible to readers of all levels. The book also includes practical examples and case studies, which are useful for those looking to apply bioinformatics techniques in their research. This book is an essential reference for anyone working in the field of bioinformatics, and is highly recommended for both beginners and experts alike.”

“Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications” Book Review: The book extensively discusses simulation techniques, with a specific emphasis on their application to biological systems. One of the significant aspects highlighted in the book is the usage of structure-based ligand design in simulations. It provides a comprehensive analysis of molecular dynamics simulations, which are essential theoretical tools in understanding biological macromolecules. The book examines potential functions in great detail, along with different methods to increase the fundamental time step in simulations that use a complete atomic representation. Moreover, practical examples are used to cover the application of molecular dynamics and free energy perturbation calculations. The book is an excellent resource for researchers and students interested in simulation techniques and their application in biological systems.

“Biomolecular Simulations: Methods and Protocols (Methods in Molecular Biology)” Book Review: The book covers many of the commonly used methods in molecular modeling of biological systems, such as electronic structure calculations, classical molecular dynamics simulations, and coarse-grained techniques. The content includes advanced techniques and recent methodological developments. Additionally, the books present well-established computational methodologies, applications to real-world biological systems, practical tips, and general protocols for conducting biomolecular simulations. One book specifically discusses cutting-edge modeling techniques, methodologies, and tools used to understand, design, and engineer nanoscale communication systems, including molecular communication systems. The other book contains a detailed explanation of simulating proteins, lipids, nucleic acids, and carbohydrates, providing both theoretical and practical knowledge to the readers.

“Biomolecular Feedback Systems” Book Review: This book serves as a comprehensive guide for advanced undergraduates, graduate students, and researchers alike. It provides a thorough overview of the principles and tools necessary for modeling, analyzing, and synthesizing biomolecular systems. The book includes an in-depth explanation of the control and dynamical systems tools utilized to analyze models. These tools encompass the analysis of equilibrium stability, limit cycles, robustness, and parameter uncertainty. The book also addresses the modular composition of synthetic circuits, providing tools for analyzing the extent of modularity and techniques for ensuring modular behavior in detail. Numerous exercises and illustrations are included throughout the book for better comprehension. As such, it can also be used as a self-contained reference for researchers.

“Modeling, Methodologies and Tools for Molecular and Nano-scale Communications” Book Review: This book is intended for graduate students and researchers who are working in the fields of computer science, biological sciences, and nanotechnology. Its content covers the fundamental principles of molecular communication, including concepts, models, and designs. It offers an in-depth exploration of specific types of molecular communication found in biological systems, such as neuronal communication in the brain. Additionally, the book focuses on various forms of nanoscale communication, including fluorescence resonance energy transfer and electromagnetic-based nanoscale communication. It also delves into the practical applications of nanomaterials in nanomedicine. The book provides a comprehensive overview of the latest developments in the emerging field of molecular and nanoscale communication.

“Practical Skills in Biomolecular Sciences” : Book Review: This book serves as an outstanding resource. It provides readers with a comprehensive understanding of the transferable skills that are essential for achieving academic excellence. The book offers practical support in developing laboratory and data analysis skills that learners will need repeatedly throughout their studies. The content covers a range of topics, including information technology, learning resources, and analytical techniques, such as advanced electrophoretic and electroanalytical techniques.

“Innovations in Biomolecular Modeling and Simulations” Book Review: The books cover a wide range of topics, including advancements in biomolecular modeling and simulation on both the algorithmic and application fronts. Among the areas covered are simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design, and other critical topics in structural biology modeling.

“Frontiers in Computational Chemistry: Volume 2: Computer Applications for Drug Design and Biomolecular Systems” Book Review: This book is tailored to meet the needs of students in various fields, including biology, chemistry, biochemistry, physics, and biophysics. Its primary goal is to showcase recent research discoveries and techniques in the dynamic field of computational chemistry, with a particular emphasis on molecular modeling strategies that are utilized in drug discovery and development. The book serves as a comprehensive collection of research, enabling researchers to stay abreast of the latest methods. Furthermore, it places a spotlight on computational chemistry approaches that can expedite drug design.

“Biomolecular Modelling and Simulations” Book Review: The book is an essential resource for protein chemists as each volume delivers updated information on protein protocols and analysis. Each volume is organized thematically and guest edited by top authorities in a broad spectrum of protein-related topics. The volume provides well-supported information accompanied by numerous high-quality illustrations, figures, and tables.

“Biomolecular Simulation: GROMOS 96 Manual and User Guide” Book Review: These books are geared towards graduate students and specialists in the fields of structural biology and chemistry, with an emphasis on presenting new and inventive approaches rather than offering comprehensive reviews on each subject. The two-volume set explores cutting-edge innovations in biomolecular modeling and simulation, encompassing both algorithmic and application fronts. Topics covered include advancements in simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design, and other vital subjects in structural biology modeling.

“Guide to Biomolecular Simulations (Focus on Structural Biology)” Book Review: This book is intended for graduate students and specialists in chemistry and structural biology, and prioritizes the presentation of new and inventive approaches over comprehensive subject reviews. The broad usage of molecular dynamics and related techniques indicates a need for an introductory, self-contained course that can help students with a basic understanding of chemistry, biology, and computer literacy to learn the basics of the field. The Guide contains twelve chapters, with the first six chapters covering the fundamentals of the field, and the remaining six chapters introducing readers to specialized but crucial applications of the methodology.

“Coarse-Graining of Condensed Phase and Biomolecular Systems” Book Review: This book targets graduate students and professionals in the fields of chemistry and structural biology, prioritizing the presentation of new and innovative approaches over comprehensive subject reviews. Each chapter concentrates on specific examples of developing coarse-graining methodologies and offers findings for various complex systems. It delves into two of the most effective coarse-graining techniques for soft matter: inverse and multiscale coarse-graining. Additionally, the book outlines ongoing development of coarse-grained models for peptides and proteins, from the amino acid level to larger length scales.

“Reconfigurable Logic: Architecture, Tools, and Applications (Devices, Circuits, and Systems)” Book Review: This book offers a comprehensive overview of the latest advancements in reconfigurable platforms, providing valuable insight into the potential future of these systems. It delves into emerging technologies that improve FPGA architectures, routing structures, and non-volatile configuration flip-flops. The book also showcases the utilization of FPGAs for high-performance systems, efficient error correction codes, and high-bandwidth network routers with built-in security. Additionally, it explores classical FPGA architectures and their supporting tools. This book provides a snapshot of the current state of the art in reconfigurable logic systems, covering a wide range of architectures, tools, and applications.

“Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications: 3 (Computer Simulations of Biomolecular Systems)” Book Review: These books are designed for graduate students and experts in structural biology and chemistry, with a focus on highlighting innovative new approaches rather than providing comprehensive reviews of each subject. The two-volume set details advancements in biomolecular modeling and simulation, covering both algorithmic and application developments. The books showcase progress and innovation in various areas, including simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design, and other significant topics in structural biology modeling.