Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
Bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the "daily practice" of an experimental research scientist.
The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.
The seven-volume set LNCS 12137, 12138, 12139, 12140, 12141, 12142, and 12143 constitutes the proceedings of the 20th International Conference on Computational Science, ICCS 2020, held in Amsterdam, The Netherlands, in June 2020.* The total of 101 papers and 248 workshop papers presented in this book set were carefully reviewed and selected from 719 submissions (230 submissions to the main track and 489 submissions to the workshops). The papers were organized in topical sections named: Part I: ICCS Main Track Part II: ICCS Main Track Part III: Advances in High-Performance Computational Earth Sciences: Applications and Frameworks; Agent-Based Simulations, Adaptive Algorithms and Solvers; Applications of Computational Methods in Artificial Intelligence and Machine Learning; Biomedical and Bioinformatics Challenges for Computer Science Part IV: Classifier Learning from Difficult Data; Complex Social Systems through the Lens of Computational Science; Computational Health; Computational Methods for Emerging Problems in (Dis-)Information Analysis Part V: Computational Optimization, Modelling and Simulation; Computational Science in IoT and Smart Systems; Computer Graphics, Image Processing and Artificial Intelligence Part VI: Data Driven Computational Sciences; Machine Learning and Data Assimilation for Dynamical Systems; Meshfree Methods in Computational Sciences; Multiscale Modelling and Simulation; Quantum Computing Workshop Part VII: Simulations of Flow and Transport: Modeling, Algorithms and Computation; Smart Systems: Bringing Together Computer Vision, Sensor Networks and Machine Learning; Software Engineering for Computational Science; Solving Problems with Uncertainties; Teaching Computational Science; UNcErtainty QUantIficatiOn for ComputationAl modeLs *The conference was canceled due to the COVID-19 pandemic.
This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.
Virtual Screening and Drug Docking, Volume 59 in the Annual Reports on Medicinal Chemistry series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including Can docking scoring functions guarantee success in virtual screening?, No dance, no partner! A tale of flexibility in docking and virtual screening, Handling Imbalance Data in Virtual Screening, Rational computational approaches to predict novel drug candidates against leishmaniasis, Virtual screening against Mtb DNA gyrase: Applications and success stories, Using Filters in Virtual Screening: A Brief Guide to Minimize Errors and Maximize Efficiency, and more. Additional chapters in the new release include Machine Learning and Deep Learning Strategies for Virtual Screening, Applications of the Virtual Screening to find the novel HIV-1 therapeutic agents, and Large-scale screening of small molecules with docking strategies and its impact on drug discovery. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Annual Reports on Medicinal Chemistry series - Updated release includes the latest information on Virtual Screening and Drug Docking
Eleven carefully selected, peer-reviewed contributions from the Virtual Conference on Computational Science (VCCS-2016) are featured in this edited book of proceedings. VCCS-2016, an annual meeting, was held online from 1st to 31st August 2016. The theme of the conference was "Computational Thinking for the Advancement of Society" and it matched the paradigm shift in the way we think. VCCS-2016 was attended by 100 participants from 20 countries. The chapters reflect a wide range of fundamental and applied research applying computational methods.
The papers collected in this volume reproduce contributions by leading sch- arstoaninternationalschoolandworkshopwhichwasorganizedandheldwith thegoaloftakinga snapshotofadiscipline undertumultuous growth. Indeed, the area of protein folding, docking and alignment is developing in response to needs for a mix of heterogeneous expertise spanning biology, chemistry, mathematics, computer science, and statistics, among others. Some of the problems encountered in this area are not only important for the scienti?c challenges they pose, but also for the opportunities they disclose intermsofmedicalandindustrialexploitation. Atypicalexampleiso?eredby protein-drug interaction (docking), a problem posing daunting computational problems at the crossroads of geometry, physics and chemistry, and, at the same time, a problem with unimaginable implications for the pharmacopoeia of the future. The schoolfocused on problems posed by the study of the mechanisms - hind protein folding, and explored di?erent ways of attacking these problems under objective evaluations of the methods. Together with a relatively small core of consolidated knowledge and tools, important re?ections were brought to this e?ort by studies in a multitude of directions and approaches. It is obviously impossible to predict which, if any, among these techniques will prove completely successful, but it is precisely the implicit dialectic among them that best conveys the current ?avor of the ?eld. Such unique diversity and richness inspired the format of the meeting, and also explains the slight departure of the present volume from the typical format in this series: the exposition of the current sediment is complemented here by a selection of quali?ed specialized contributions.
