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Vertebrate and invertebrate respiratory proteins, lipoproteins and other body fluid proteins

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TLDR
This book focuses on respiratory proteins, the broad hemoglobin family, as well as the molluscan and arachnid hemocyanins (and their multifunctional roles) and a number of other proteins, such as the hemerythrins; serum albumin; serum amyloid A; von Willebrand factor and its interaction with factor VIII; and C-reactive protein.
Abstract
This book focuses on respiratory proteins, the broad hemoglobin family, as well as the molluscan and arachnid hemocyanins (and their multifunctional roles). Featuring 20 chapters addressing invertebrate and vertebrate respiratory proteins, lipoproteins and other body fluid proteins, and drawing on the editors' extensive research in the field, it is a valuable addition to the Subcellular Biochemistry book series. The book covers a wide range of topics, including lipoprotein structure and lipid transport; diverse annelid, crustacean and insect defense proteins; and insect and vertebrate immune complexes. It also discusses a number of other proteins, such as the hemerythrins; serum albumin; serum amyloid A; von Willebrand factor and its interaction with factor VIII; and C-reactive protein. Given its scope, the book appeals to biologists, biomedical scientists and clinicians, as well as advanced undergraduates and postgraduates in these disciplines. Available as a printed book and also as an e-book and e-chapters, the fascinating material included is easily accessible.

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References
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MUSCLE: multiple sequence alignment with high accuracy and high throughput

TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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UCSF Chimera--a visualization system for exploratory research and analysis.

TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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The Protein Data Bank

TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies

TL;DR: It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.
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On the Nature of Allosteric Transitions: A Plausible Model

TL;DR: "It is certain that all bodies whatsoever, though they have no sense, yet they have perception, and whether the body be alterant or alterec, evermore a perception precedeth operation; for else all bodies would be like one to another."