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Book
xxii, 474 p., [8] p. of plates : ill. (some col.) ; 25 cm.
  • 1. Introduction-- 2. Genome organization and evolution-- 3. Scientific publications and archives: media, content and access-- 4. Archives and information retrieval-- 5. Alignments and phylogenetic trees-- 6. Structural bioinformatics and drug discovery-- 7. Proteomics and systems biology.
  • (source: Nielsen Book Data)9780199208043 20160528
Life in a post-genomic age has the promise to revolutionize our understanding of how our genes shape who we are, how our genome evolved, and how we function. There are new possibilities for an improved quality of life as we exploit new knowledge to design novel, more effective drugs. Central to these possibilities being realized is one of the most important information-gathering, data-mining, and knowledge-building tools in current research and healthcare development: bioinformatics. An Introduction to Bioinformatics introduces students to the immense power of bioinformatics as a set of scientific tools. The book explains how to access the data archives of genomes and proteins, and the kinds of questions these data and tools can answer: how to make inferences from the data archives, to make connections among them, and to derive useful and interesting predictions. Blending factual content with many opportunities for active learning, Introduction to Bioinformatics offers a truly reader-friendly way to get to grips with this subject, making it the ideal resource for anyone new to the field. Online Resource Centre: The Online Resource Centre features the following materials: For lecturers (password protected): * Figures from the book available to download, to facilitate lecture slide preparation For students: * Hyperlinked bibliography - online links to articles referenced in the book, encouraging student engagement with the primary literature * Links to PDB structures of all proteins cited in the book, to enable students to investigate the 3D structures of proteins in a visual, interactive way * Data from the book in computer-readable form, which is available for instant use to facilitate hands-on learning by the student - Guidance to help students answer problems from the text, to support and encourage self-directed learning.
(source: Nielsen Book Data)9780199208043 20160528
Engineering Library (Terman), eReserve
APPPHYS-315-01
Book
xv, 349 p. : ill. ; 25 cm.
  • BLAST and FASTA.- Sequence Alignment.- Contig Assembly.- DNA Replication and Viral Evolution.- Gene and Motif Prediction.- Hidden Markov Models.- Gibbs Sampler.- Bioinformatics and Vertebrate Mitochondria.- Characterizing Translation Efficiency.- Protein Isoelectric Point.- Bioinformatics and Two-Dimensional Protein Separation.- Self-Organizing Map and Other Clustering Algorithms.- Molecular Phylogenetics.- Fundamentals of Proteomics.
  • (source: Nielsen Book Data)9780387713366 20160528
The many books that have been written on bioinformatics tend to fall on two extremes: books that feature computational details with a great deal of mathematics, for computational scientists and mathematicians, or books that treat bioinformatics mostly as a giant black box, for biologists. Previous books written on bioinformatics often have limited contribution to creating interdisciplinary scientists needed in modern biological and biomedical sciences. This book aims to render both mathematical equations and biology to numbers, to help truly interdisciplinary scientists. Although the book covers bioinformatics methods at a level more advanced than most other bioinformatics books, the extensive numerical illustration of these methods should make it accessible to most senior undergraduate students and graduate students majoring in science and software engineering. Nearly all algorithms in the book are implemented in a free and user-friendly computer program (DAMBE).
(source: Nielsen Book Data)9780387713366 20160528
Engineering Library (Terman), eReserve
APPPHYS-315-01
Book
xvi, 603, A63 p. : ill. ; 24 cm. + 1 CD-ROM (3 1/4 in.)
Engineering Library (Terman), Science Library (Li and Ma)
APPPHYS-315-01
Book
xi, 339 p. : ill. (some col.) ; 27 cm.
  • Introduction to biological databases
  • Pairwise sequence alignment
  • Database similarity searching
  • Multiple sequence alignment
  • Profiles and hidden Markov models
  • Protein motifs and domain prediction
  • Gene prediction
  • Promoter and regulatory element prediction
  • Phylogenetics basics
  • Phylogenetic tree construction methods and programs
  • Protein structure basics
  • Protein structure visualization, comparision, and classification
  • Protein secondary structure prediction
  • Protein tertiary structure prediction
  • RNA structure prediction
  • Genome mapping, assembly, and comparison
  • Functional genomics
  • Proteomics.
Cambridge Core Access limited to 3 simultaneous users.
Engineering Library (Terman), eReserve
APPPHYS-315-01
Book
xxii, 195 p. : ill. ; 28 cm.
  • 1. From Sequence to Structure:.Overview: Protein Function and Architecture.Amino Acids.Genes and Proteins.The Peptide Bond.Bonds that Stablize Folded Proteins.Importance and Determinants of Secondary Structure.Properties of the Alpha Helix.Properties of the Beta Sheet.Prediction of Secondary Structure.Folding.Tertiary Structure.Membrane Protein Structure.Protein Stability 1: Weak Interactions and Flexibility.Protein Stability 2: Post-Translational Modifications.The Protein Domain.The Universe of Protein Structures.Protein Motifs.Alpha Domains and Beta Domains.Alpha/Beta, Alpha+Beta and Cross-Linked Domains.Quaternary Structure: General Principles.Quaternary Structure: Intermolecular Interfaces.Quaternary Structure: Geometry.Protein Flexibility.2. From Structure to Function:.Overview: The Structural Basis of Protein Function.Recognition, Complementarity and Active Sites.Flexibility and Protein Function.Location of Binding Sites.Nature of Binding Sites.Functional Properties of Structural Proteins.Catalysis: Overview.Active-site Geometry.Proximity and Ground-State Destabilization.Stabilization of Transition States and Exclusion of Water.Redox Reaction.Addition/Elimination, Hydrolysis and Decarboxylation.Active-Site Chemistry.Cofactors.Multi-Step Reactions.Multifunctional Enzymes.Multifunctional Enzymes with Tunnels.3. Control of Protein Function:.Overview: Mechanisms of Regulation.Protein Interaction Domains.Regulation by Location.Control by pH and Redox Environment.Effector Ligands: Competitive Binding and Cooperativity.Effector Ligands: Conformational Change and Allostery.Protein Switches Based on Nucleotide Hydrolysis.GTPase Switches: Small Signaling G proteins.GTPase Switches: Signal Relay by Heterotrimeric GTPases.Gtpase Switches: Protein Synthesis.Motor Protein Switches.Regulation by Degradation.Control of Protein Function by Phosphorylation.Regulation of Signaling Protein Kinases: Activation Mechnism.Regulation of Signaling Protein Kinases: Cdk Activation.Two-Component Signaling Systems in Bacteria.Control by Proteolysis: Activation of Precursors.Protein Splicing: Autoproteolysis by Inteins.Glycosylation.Protein Targeting by Lipid Modification.Methylation, N-acetylation, Sumoylation and Nitrosylation.4. From Sequence to Function:.Overview: From Sequence to Function in the Age of Genomics.Sequence Alignment and Comparison.Protein Profiling.Deriving Function from Sequence.Experimental Tools for Probing Protein Function.Divergent and Convergent Evolution.Structure from Sequence: Homology Modeling.Structure from Sequence: Profile-Based Threading and "Rosetta".Deducing Function from Structure: Protein Superfamilies.Strategies for Identifying Binding Sites.Strategies for Identifying Catalytic Residues.TIM Barrels: One Structure with Diverse Functions.PLP Enzymes: Diverse Structures with One Function.Moonlighting: Proteins with More Than One Function.Chameleon Sequences: One Sequence with More than One Fold.Prions, Amyloids and Serpins: Metastable Protein Folds.Functions for Uncharacterized Genes: Galactonate Dehydratase.Starting from Scratch: A Gene Product of Unknown Function.5. Structure Determination:.The Interpretation of Structural Information.Structure Determination by X-Ray Crystallography and NWR.Quality and Representation of Crystal and NMR Structures.
  • (source: Nielsen Book Data)9781405119221 20160527
  • 1. From Sequence to Structure-- 2. From Structure to Function-- 3. Control of Protein Function-- 4. From Sequence to Function: Case Studies in Structural and Functional Genomics-- 5. Structure Determination.
  • (source: Nielsen Book Data)9780199556847 20160528
"Protein Structure and Function" considers the key concepts of protein structure and function and the relationship between sequence, structure and function with clear, concise explanations and full colour illustrations. It is written by two outstanding names in the field, Gregory Petsko and Dagmar Ringe. It considers the principles of protein structure and folding, functional properties of proteins and regulation of protein function, and introduces the basic principles whereby structure and function are deduced from sequence. This work is fully up-to-date with emphasis on what sequence can tell you about structure and function. It is ideal for undergraduates and graduates studying the fundamental principles of protein structure and function in departments of biochemistry and molecular biology, and working scientists needing an up-to-date introduction to the field.All 240 illustrations from "Protein Structure and Function" are available on the web as jpgs and downloadable tifs for teaching.
(source: Nielsen Book Data)9781405119221 20160527
Intended for upper-level undergraduate and beginning graduate students, this primer introduces the general principles of protein structure, folding, and function and explains the conceptual basis for inferring structure and function from genomic sequence. Employing a modular design, chapters are div.
(source: Nielsen Book Data)9780878936632 20160527
How does the chemical description of a protein relate to its three-dimensional structure? How does the three-dimensional structure relate to the machinery that brings about a chemical reaction? How does the sequence of a gene encode not only the sequence of a protein but, more importantly, the architecture and function of that protein? Protein Structure and Function provides a clear and critical survey of our current understanding of the structure and function of proteins to answer questions such as these. Opening with a consideration of the link between protein sequence and structure, it goes on to explore the structural basis of protein function and how this function is controlled. Finally, it examines a range of case studies that illuminate the range of roles performed by proteins, and the diverse structures these proteins exhibit.Protein Structure and Function combines articulate prose with striking full colour illustrations, while the unique Primers in Biology modular structure integrates text, illustrations, definitions, and literature references for each topic into one double-page spread, bringing to the student's fingertips all the tools that they need to master that topic. Online Resource Centre The Online Resource Centre features figures from the book available to download, for registered adopters of the book.
(source: Nielsen Book Data)9780199556847 20160528
Engineering Library (Terman)
APPPHYS-315-01