Methods And Applications In Computational Protein Design
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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 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.
Multistate Computational Protein Design
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Author : James A. Davey
language : en
Publisher:
Release Date : 2016
Multistate Computational Protein Design written by James A. Davey and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Computational Structural Biology
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Author : Manuel Claude Peitsch
language : en
Publisher: World Scientific
Release Date : 2008
Computational Structural Biology written by Manuel Claude Peitsch and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.
This work covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology.
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.
Protein Design
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Author : Raphael Guerois
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-04
Protein Design written by Raphael Guerois and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-02-04 with Science categories.
Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success. The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins.
Computational Protein Design
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Author : Zhixiu Li
language : en
Publisher:
Release Date : 2015
Computational Protein Design written by Zhixiu Li and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with Computational biology categories.
Computational protein design aims at designing amino acid sequences that can fold into a target structure and perform a desired function. Many computational design methods have been developed and their applications have been successful during past two decades. However, the success rate of protein design remains too low to be of a useful tool by biochemists whom are not an expert of computational biology. In this dissertation, we first developed novel computational assessment techniques to assess several state-of-the-art computational techniques. We found that significant progresses were made in several important measures by two new scoring functions from RosettaDesign and from OSCAR-design, respectively. We also developed the first machine-learning technique called SPIN that predicts a sequence profile compatible to a given structure with a novel nonlocal energy-based feature. The accuracy of predicted sequences is comparable to RosettaDesign in term of sequence identity to wild type sequences. In the last two application chapters, we have designed self-inhibitory peptides of Escherichia coli methionine aminopeptidase (EcMetAP) and de novo designed barstar. Several peptides were confirmed inhibition of EcMetAP at the micromole-range 50% inhibitory concentration. Meanwhile, the assessment of designed barstar sequences indicates the improvement of OSCAR-design over RosettaDesign.
Peptide And Protein Design For Biopharmaceutical Applications
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Author : Knud Jensen
language : en
Publisher: John Wiley & Sons
Release Date : 2009-09-01
Peptide And Protein Design For Biopharmaceutical Applications written by Knud Jensen and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-09-01 with Science categories.
Peptides serve as effective drugs in the clinic today. However the inherent drawbacks of peptide structures can limit their efficacy as drugs. To overcome this researchers are developing new methods to create ‘tailor-made’ peptides and proteins with improved pharmacological properties. Design of Peptides and Proteins provides an overview of the experimental and computational methods for peptide and protein design, with an emphasis on specific applications for therapeutics and biomedical research. Topics covered include: Computer modeling of peptides and proteins Peptidomimetics Design and synthesis of cyclic peptides Carbohydrates in peptide and protein design De novo design of peptides and proteins Medical development applications An extended case study – the design of insulin variants Design of Peptides and Proteins presents the state-of-the-art of this exciting approach for therapeutics, with contributions from international experts. It is an essential resource for academic and industrial scientists in the fields of peptide and protein drug design, biomedicine, biochemistry, biophysics, molecular modelling, synthetic organic chemistry and medicinal/pharmaceutical chemistry.
Methods In Protein Design
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Author :
language : en
Publisher: Academic Press
Release Date : 2013-02-14
Methods In Protein Design written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-02-14 with Science categories.
This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. This volume covers methods in protein design and it has chapters on such topics as protein switch engineering by domain insertion, evolution based design of proteins, and computationally designed proteins. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers methods in protein design Contains chapters with such topics as protein switch engineering by domain insertion, evolution-based design of proteins, and computationally designed proteins
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-05-05
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-05-05 with Science categories.
Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.