Download or read book Energy Functions for Protein Design written by Sivarama Krishna Pokala and published by . This book was released on 2001 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Automated Design of Energy Functions for Protein Structure Prediction by Means of Genetic Programming and Improved Structure Similarity Assessment written by Paweł Widera and published by . This book was released on 2010 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Automated Design of Energy Functions for Protein Structure Prediction by Means of Genetic Programming and Improved Structure Similarity Assessment written by Pawel Widera and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of protein structure prediction is a crucial part of understanding the function of the building blocks of life. It is based on the approximation of a protein free energy that is used to guide the search through the space of protein structures towards the thermodynamic equilibrium of the native state. A function that gives a good approximation of the protein free energy should be able to estimate the structural distance of the evaluated candidate structure to the protein native state. This correlation between the energy and the similarity to the native is the key to high quality predictions. State-of-the-art protein structure prediction methods use very simple techniques to design such energy functions. The individual components of the energy functions are created by human experts with the use of statistical analysis of common structural patterns that occurs in the known native structures. The energy function itself is then defined as a simple weighted sum of these components. Exact values of the weights are set in the process of maximisation of the correlation between the energy and the similarity to the native measured by a root mean square deviation between coordinates of the protein backbone. In this dissertation I argue that this process is oversimplified and could be improved on at least two levels. Firstly, a more complex functional combination of the energy components might be able to reflect the similarity more accurately and thus improve the prediction quality. Secondly, a more robust similarity measure that combines different notions of the protein structural similarity might provide a much more realistic baseline for the energy function optimisation. To test these two hypotheses I have proposed a novel approach to the design of energy functions for protein structure prediction using a genetic programming algorithm to evolve the energy functions and a structural similarity consensus to provide a reference similarity measure. The best evolved energy functions were found to reflect the similarity to the native better than the optimised weighted sum of terms, and therefore opening a new interesting area of research for the machine learning techniques.
Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book De Novo Protein Structure Modeling and Energy Function Design written by Lin Chen and published by . This book was released on 2015 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Design written by Raphael Guerois and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Effective Energy Functions for Protein Structure Prediction Based on Predicted Structural Features written by Arlo Randall and published by . This book was released on 2008 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: SELECTpro, ABIpro, 3Dpro, and TMBpro are all freely available to the prediction community through: www.igb.uci.edu/servers/psss.html.
Download or read book Methods in Protein Design written by and published by Academic Press. This book was released on 2013-02-14 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.
Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Download or read book Protein Engineering and Design written by Paul R. Carey and published by Elsevier. This book was released on 1996-06-21 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: The design and production of novel peptides and proteins occupy pivotal positions in science and technology and will continue to do so in the 21st century. Protein Engineering and Design outlines the rapid advances in computer-based modeling, protein engineering, and methods needed for protein and peptide preparation and characterization. This indispensable reference lays the groundwork for understanding this multidisciplinary activity while providing an introduction for researchers and students to the field of protein design. Introduces and defines the techniques involved in protein engineering and design Provides a concise overview of key technologies involved and demonstrates their contributions to the specialized design and production of novel proteins and peptides
Download or read book Protein Design from in Silico to in Vivo written by Arnab Bula Chowdry and published by . This book was released on 2008 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Structure Prediction by Optimization of Energy Functions written by Nir Kalisman and published by . This book was released on 2008 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mathematical Methods for Protein Structure Analysis and Design written by Concettina Guerra and published by Springer Science & Business Media. This book was released on 2003-06-25 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The papers collected in this volume reproduce contributions by leading sch- arstoaninternationalschoolandworkshopwhichwasorganizedandheldwith thegoaloftakinga snapshotofadiscipline undertumultuous growth. Indeed, the area of protein folding, docking and alignment is developing in response to needs for a mix of heterogeneous expertise spanning biology, chemistry, mathematics, computer science, and statistics, among others. Some of the problems encountered in this area are not only important for the scienti?c challenges they pose, but also for the opportunities they disclose intermsofmedicalandindustrialexploitation. Atypicalexampleiso?eredby protein-drug interaction (docking), a problem posing daunting computational problems at the crossroads of geometry, physics and chemistry, and, at the same time, a problem with unimaginable implications for the pharmacopoeia of the future. The schoolfocused on problems posed by the study of the mechanisms - hind protein folding, and explored di?erent ways of attacking these problems under objective evaluations of the methods. Together with a relatively small core of consolidated knowledge and tools, important re?ections were brought to this e?ort by studies in a multitude of directions and approaches. It is obviously impossible to predict which, if any, among these techniques will prove completely successful, but it is precisely the implicit dialectic among them that best conveys the current ?avor of the ?eld. Such unique diversity and richness inspired the format of the meeting, and also explains the slight departure of the present volume from the typical format in this series: the exposition of the current sediment is complemented here by a selection of quali?ed specialized contributions.
Download or read book Protein Design and Structure written by Rossen Donev and published by Academic Press. This book was released on 2022-05-06 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Design and Structure, Volume 130 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Advances in Protein Chemistry and Structural Biology series Includes the latest information on protein design and structure
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A Physics based Energy Function for Ab Initio Protein Structure Prediction and Refinement written by Matthew Shihhsiu Lin and published by . This book was released on 2009 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
