Large Scale Computational Protein Design
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Large Scale Computational Protein Design
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Author : Stefan Mathias Larson
language : en
Publisher:
Release Date : 2004
Large Scale Computational Protein Design written by Stefan Mathias Larson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Computational Protein Design
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Author : Ilan Samish
language : en
Publisher: Humana
Release Date : 2016-12-03
Computational Protein Design written by Ilan Samish and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-12-03 with Science categories.
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Computational Design Of Protein Structure And Prediction Of Ligand Binding
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Author : Robert Aron Broom
language : en
Publisher:
Release Date : 2017
Computational Design Of Protein Structure And Prediction Of Ligand Binding written by Robert Aron Broom and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Ligand binding (Biochemistry) categories.
Proteins perform a tremendous array of finely-tuned functions which are not only critical in living organisms, but can be used for industrial and medical purposes. The ability to rationally design these molecular machines could provide a wealth of opportunities, for example to improve human health and to expand the range and reduce cost of many industrial chemical processes. The modularity of a protein sequence combined with many degrees of structural freedom yield a problem that can frequently be best tackled using computational methods. These computational methods, which include the use of: bioinformatics analysis, molecular dynamics, empirical forcefields, statistical potentials, and machine learning approaches, amongst others, are collectively known as Computational Protein Design (CPD). Here CPD is examined from the perspective of four different goals: successful design of an intended structure, the prediction of folding and unfolding kinetics from structure (kinetic stability in particular), engineering of improved stability, and prediction of binding sites and energetics. A considerable proportion of protein folds, and the majority of the most common folds ("superfolds"), are internally symmetric, suggesting emergence from an ancient repetition event. CPD, an increasingly popular and successful method for generating de novo folded sequences and topologies, suffers from exponential scaling of complexity with protein size. Thus, the overwhelming majority of successful designs are of relatively small proteins ( 100 amino acids). Designing proteins comprised of repeated modular elements allows the design space to be partitioned into more manageable portions. Here, a bioinformatics analysis of a "superfold", the beta-trefoil, demonstrated that formation of a globular fold via repetition was not only an ancient event, but an ongoing means of generating diverse and functional sequences. Modular repetition also promotes rapid evolution for binding multivalent targets in the "evolutionary arms race" between host and pathogen. Finally, modular repetition was used to successfully design, on the first attempt, a well-folded and functional beta-trefoil, called ThreeFoil. Improving protein design requires understanding the outcomes of design and not simply the 3D structure. To this end, I undertook an extensive biophysical characterization of ThreeFoil, with the key finding that its unfolding is extraordinarily slow, with a half-life of almost a decade. This kinetic stability grants ThreeFoil near-immunity to common denaturants as well as high resistance to proteolysis. A large scale analysis of hundreds of proteins, and coarse-grained modelling of ThreeFoil and other beta-trefoils, indicates that high kinetic stability results from a folded structure rich in contacts between residues distant in sequence (long-range contacts). Furthermore, an analysis of unrelated proteins known to have similar protease resistance, demonstrates that the topological complexity resulting from these long-range contacts may be a general mechanism by which proteins remain folded in harsh environments. Despite the wonderful kinetic stability of ThreeFoil, it has only moderate thermodynamic stability. I sought to improve this in order to provide a stability buffer for future functional engineering and mutagenesis. Numerous computational tools which predict stability change upon point mutation were used, and 10 mutations made based on their recommendations. Despite claims of 80% accuracy for these predictions, only 2 of the 10 mutations were stabilizing. An in-depth analysis of more than 20 such tools shows that, to a large extent, while they are capable of recognizing highly destabilizing mutations, they are unable to distinguish between moderately destabilizing and stabilizing mutations. Designing protein structure tests our understanding of the determinants of protein folding, but useful function is often the final goal of protein engineering. I explored protein-ligand binding using molecular dynamics for several protein-ligand systems involving both flexible ligand binding to deep pockets and more rigid ligand binding to shallow grooves. I also used various levels of simulation complexity, from gas-phase, to implicit solvent, to fully explicit solvent, as well as simple equilibrium simulations to interrogate known interactions to more complex energetically biased simulations to explore diverse configurations and gain novel information.
Computational Protein Design
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Author : Ilan Samish
language : en
Publisher: Methods in Molecular Biology
Release Date : 2018-12-17
Computational Protein Design written by Ilan Samish and has been published by Methods in Molecular Biology this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-17 with Science categories.
Protein Engineering And Design
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Author : Sheldon J. Park
language : en
Publisher: CRC Press
Release Date : 2009-09-25
Protein Engineering And Design written by Sheldon J. Park and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-25 with Medical categories.
Experimental protein engineering and computational protein design are broad but complementary strategies for developing proteins with altered or novel structural properties and biological functions. By describing cutting-edge advances in both of these fields, Protein Engineering and Design aims to cultivate a synergistic approach to protein science
Introduction To Computational Proteomics
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Author : Golan Yona
language : en
Publisher: CRC Press
Release Date : 2010-12-09
Introduction To Computational Proteomics written by Golan Yona and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-09 with Mathematics categories.
Introduction to Computational Proteomics introduces the field of computational biology through a focused approach that tackles the different steps and problems involved with protein analysis, classification, and meta-organization. The book starts with the analysis of individual entities and works its way through the analysis of more complex entitie
Advances In Computational Protein Design
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Author : Geoffrey Hom
language : en
Publisher:
Release Date : 2005
Advances In Computational Protein Design written by Geoffrey Hom and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with Electronic dissertations categories.
Computational Protein Design
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Author : Elijah Joshua
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2017-06-13
Computational Protein Design written by Elijah Joshua and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-06-13 with categories.
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Methods And Applications In Computational Protein Design
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Author : Jason Charles Biddle
language : en
Publisher:
Release Date : 2010
Methods And Applications In Computational Protein Design written by Jason Charles Biddle and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
In this thesis, we summarize our work on applications and methods for computational protein design. First, we apply computational protein design to address the problem of degradation in stored proteins. Specifically, we target cysteine, asparagine, glutamine, and methionine amino acid residues to reduce or eliminate a protein's susceptibility to degradation via aggregation, deamidation, and oxidation. We demonstrate this technique on a subset of degradation-prone amino acids in phosphotriesterase, an enzyme that hydrolyzes toxic organophosphates including pesticides and chemical warfare agents. Second, we introduce BroMAP/A*, an exhaustive branch-and- bound search technique with enumeration. We compare performance of BroMAP/A* to DEE/A*, the current standard for conformational search with enumeration in the protein design community. When limited computational resources are available, DEE/A* sometimes fails to find the global minimum energy conformation and/or enumerate the lowest-energy conformations for large designs. Given the same computational resources, we show how BroMAP/A* is able to solve large designs by efficiently dividing the search space into small, solvable subproblems.
Computational Protein Protein Interactions
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Author : Ruth Nussinov
language : en
Publisher: CRC Press
Release Date : 2009-06-26
Computational Protein Protein Interactions written by Ruth Nussinov and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-26 with Science categories.
Often considered the workhorse of the cellular machinery, proteins are responsible for functions ranging from molecular motors to signaling. The broad recognition of their involvement in all cellular processes has led to focused efforts to predict their functions from sequences, and if available, from their structures. An overview of current resear