Protein informatics is a newer name for an already existing discipline. It encompasses the techniques used in bioinformatics and molecular modeling that are related to proteins. While bioinformatics is mainly concerned with the collection, organization, and analysis of biological data, molecular modeling is devoted to representation and manipulation of the structure of proteins. Protein informatics requires substantial prerequisites on computer science, mathematics, and molecular biology. The approach chosen here, allows a direct and rapid grasp on the subject starting from basic knowledge of algorithm design, calculus, linear algebra, and probability theory. An Introduction to Protein Informatics, a professional monograph will provide the reader a comprehensive introduction to the field of protein informatics. The text emphasizes mathematical and computational methods to tackle the central problems of alignment, phylogenetic reconstruction, and prediction and sampling of protein structure. An Introduction to Protein Informatics is designed for a professional audience, composed of researchers and practitioners within bioinformatics, molecular modeling, algorithm design, optimization, and pattern recognition. This book is also suitable as a graduate-level text for students in computer science, mathematics, and biomedicine.

Bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, Proteome Informatics will provide a detailed introduction to the main informatics topics that underpin the various LC-MS/MS protocols used for protein identification and quantitation.

Proteins fold in interesting and intriguing ways. Importantly, the structure of a protein can provide additional clues to its function(s) than does its sequence alone. Scientists interested in characterizing a novel protein sequence should therefore not only familiarize themselves with computer tools and methods for sequence analysis but also with those for structure analysis. Computer scientists interested in developing software tools for bioinformatics will find that structure analysis is no less interesting and challenging than sequence analysis. Both scientists and computer scientists will note that the field of protein structure analysis is going to become increasingly important in coming years, now that the post-genomic era is here. This short book introduces the topic of protein structure informatics in two parts. Part I covers the main public-domain protein structure databases, and associated tools such as structure viewers and search tools. Part II covers problems and algorithms for aligning a structure to a structure, a sequence to a structure, for predicting a structure for a sequence, on "protein structure profiles", and the molecular docking problem. All chapters contain references for further reading. This book has been cooking slowly for more than two years. Over this period, it has undergone numerous revisions and refinements. The material has also been presented and refined in classes taught by the author at the University of California, Santa Cruz extension.

A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.

Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012

Pairwise global alignment of sequences. Pairwise local alignment and database search. Statical analysis. Multiple global alignment and phylogenetic trees. Scoring matrices. Profiles. Sequence patterns. Structures and structure descriptions. Superposition and Dynamic programming. Geometric techniques. Clustering: Combining local similarities. Significance and assessment of structure comparisons. Multiple structure comparison. Protein structure classification. Structure prediction: Threading. Basics in mathematics, probability and algorithms. Introduction to molecular biology.