Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations. Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking. Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.

This eBook is dedicated to Prof. William L. Hase, who passed away on Monday, March 23, 2020.

This volume looks at modern computational strategies and techniques used in GPCR drug discovery including structure and ligand-based approaches and cheminformatics. The chapters in this book describe how these approaches can be applied to address key drug discovery issues, such as receptor structure modelling, function and dynamics, prediction of protein-water-ligand interactions and binding kinetics, free energy of binding, interconversion between agonists and antagonists, deorphanization of GPCRs, and the discovery of biased and allosteric modulators. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modelling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique,Computational Methods for GPCR Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.

EACM is a comprehensive reference work covering the vast field of applied and computational mathematics. Applied mathematics itself accounts for at least 60 per cent of mathematics, and the emphasis on computation reflects the current and constantly growing importance of computational methods in all areas of applications. EACM emphasizes the strong links of applied mathematics with major areas of science, such as physics, chemistry, biology, and computer science, as well as specific fields like atmospheric ocean science. In addition, the mathematical input to modern engineering and technology form another core component of EACM.

This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolboxTM. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence comparison, scoring, and determining evolutionary distance. The main focus of the third part is on modeling biological sequences and patterns as Markov chains. It presents key principles for analyzing and searching for sequences of significant motifs and biomarkers. The last part of the book, dedicated to systems biology, covers phylogenetic analysis and evolutionary tree computations, as well as gene expression analysis with microarrays. In brief, the book offers the ideal hands-on reference guide to the field of bioinformatics and computational biology.

This book provides a broad and nuanced overview of the achievements and legacy of Professor William (“Bill”) Goddard in the field of computational materials and molecular science. Leading researchers from around the globe discuss Goddard’s work and its lasting impacts, which can be seen in today’s cutting-edge chemistry, materials science, and biology techniques. Each section of the book closes with an outline of the prospects for future developments. In the course of a career spanning more than 50 years, Goddard’s seminal work has led to dramatic advances in a diverse range of science and engineering fields. Presenting scientific essays and reflections by students, postdoctoral associates, collaborators and colleagues, the book describes the contributions of one of the world’s greatest materials and molecular scientists in the context of theory, experimentation, and applications, and examines his legacy in each area, from conceptualization (the first mile) to developments and extensions aimed at applications, and lastly to de novo design (the last mile). Goddard’s passion for science, his insights, and his ability to actively engage with his collaborators in bold initiatives is a model for us all. As he enters his second half-century of scientific research and education, this book inspires future generations of students and researchers to employ and extend these powerful techniques and insights to tackle today’s critical problems in biology, chemistry, and materials. Examples highlighted in the book include new materials for photocatalysts to convert water and CO2 into fuels, novel catalysts for the highly selective and active catalysis of alkanes to valuable organics, simulating the chemistry in film growth to develop two-dimensional functional films, and predicting ligand–protein binding and activation to enable the design of targeted drugs with minimal side effects.

A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.

The optimization of pharmacokinetic properties has become the bottleneck and a major challenge in drug research. There was, hence, an urgent need for a book covering this field in an authoritative, comprehensive, factual, and conceptual manner. In this work of unique breadth and depth, international authorities and practicing experts from academia and industry present the most modern biological, physicochemical, and computational strategies to achieve optimal pharmacokinetic properties in research series. These properties include gastrointestinal absorption, protein binding, brain permeation, and metabolic profile. Toxicological issues are, of course, also of utmost importance. In addition to its 33 chapters, the book includes a CD-ROM containing the invited lectures, oral communications and posters (in full version) presented at the Second LogP Symposium, 'Lipophilicity in Drug Disposition -- Practical and Computational Approaches to Molecular Properties Related to Drug Permeation, Disposition and Metabolism', held at the University of Lausanne in March 2000.n̓.

Global Optimization has emerged as one of the most exciting new areas of mathematical programming. Global optimization has received a wide attraction from many fields in the past few years, due to the success of new algorithms for addressing previously intractable problems from diverse areas such as computational chemistry and biology, biomedicine, structural optimization, computer sciences, operations research, economics, and engineering design and control. The chapters in this volume focus on recent deterministic methods and stochastic methods for global optimization, distributed computing methods in global optimization, and applications of global optimization in several branches of applied science and engineering, computer science, computational chemistry, structural biology, and bio-informatics.