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Multi Regional Analysis Of Contact Maps For Protein Structure Prediction
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Book Synopsis Multi-regional Analysis of Contact Maps for Protein Structure Prediction by : Hazem Radwan Abdal-Rehiem Ahmed
Download or read book Multi-regional Analysis of Contact Maps for Protein Structure Prediction written by Hazem Radwan Abdal-Rehiem Ahmed and published by . This book was released on 2009 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1D protein sequences, 2D contact maps and 3D structures are three different representational levels of detail for proteins. Predicting protein 3D structures from their 1D sequences remains one of the complex challenges of bioinformatics. The "Divide and Conquer" principle is applied in our research to handle this challenge, by dividing it into two separate yet dependent subproblems, using a Case-Based Reasoning (CBR) approach. Firstly, 2D contact maps are predicted from their 1D protein sequences; secondly, 3D protein structures are then predicted from their predicted 2D contact maps. We focus on the problem of identifying common substructural patterns of protein contact maps, which could potentially be used as building blocks for a bottom-up approach for protein structure prediction. We further demonstrate how to improve identifying these patterns by combining both protein sequence and structural information. We assess the consistency and the efficiency of identifying common substructural patterns by conducting statistical analyses on several subsets of the experimental results with different sequence and structural information.
Book Synopsis Prediction of Protein Secondary Structure by : Yaoqi Zhou
Download or read book Prediction of Protein Secondary Structure written by Yaoqi Zhou and published by Humana. This book was released on 2016-10-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.
Book Synopsis Nearest-neighbor Methods in Learning and Vision by : Gregory Shakhnarovich
Download or read book Nearest-neighbor Methods in Learning and Vision written by Gregory Shakhnarovich and published by . This book was released on 2005 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text presents theoretical and practical discussions of nearest neighbour (NN) methods in machine learning and examines computer vision as an application domain in which the benefit of these advanced methods is often dramatic.
Book Synopsis Protein Structure Analysis Using Contact Maps and Secondary Structure by : Patrick May
Download or read book Protein Structure Analysis Using Contact Maps and Secondary Structure written by Patrick May and published by . This book was released on 2007 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Structure by Distance Analysis by : Henrik Bohr
Download or read book Protein Structure by Distance Analysis written by Henrik Bohr and published by IOS Press. This book was released on 1994 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Theory and Applications of Distance Geometry by : Leonard M. Blumenthal
Download or read book Theory and Applications of Distance Geometry written by Leonard M. Blumenthal and published by . This book was released on 1900 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Distance Geometry and Molecular Conformation by : G. M. Crippen
Download or read book Distance Geometry and Molecular Conformation written by G. M. Crippen and published by John Wiley & Sons. This book was released on 1988 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA 3D Structure Analysis and Prediction by : Neocles Leontis
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Book Synopsis Protein Structure Prediction by : Daisuke Kihara
Download or read book Protein Structure Prediction written by Daisuke Kihara and published by Humana. This book was released on 2021-07-18 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough new edition explores web servers and software for protein structure prediction and modeling that are freely available to the academic community. Taking into account the numerous advances in the computational protein structure prediction/modeling field, the book includes residue-contact prediction via deep learning, a wide variety of protein docking models, as well as cryo-electron microscopy (cryo-EM) techniques. Written by renowned experts in the field and for the highly successful Methods in Molecular Biology series, chapters include the kind of key detail and implementation advice necessary for researchers to achieve optimal results in their own work. Authoritative and fully updated, Protein Structure Prediction, Fourth Edition is a practical and immediately useful guide for biology researchers working toward modeling protein structures./div/div/div/div/div/div/div/div/div/div/div/div/div/div/div/div/divdiv
Book Synopsis Machine Learning for Peptide Structure, Function, and Design by : Ruiquan Ge
Download or read book Machine Learning for Peptide Structure, Function, and Design written by Ruiquan Ge and published by Frontiers Media SA. This book was released on 2022-11-07 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The PyRosetta Interactive Platform for Protein Structure Prediction and Design by : Jeffrey J Gray
Download or read book The PyRosetta Interactive Platform for Protein Structure Prediction and Design written by Jeffrey J Gray and published by Createspace Independent Publishing Platform. This book was released on 2014-08-26 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: TALARIS UPDATE INCLUDED ... This book contains a set of workshops which teach the PyRosetta program for computational protein structure prediction and design. PyRosetta (http: //www.pyrosetta.org) is a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite. Rosetta, developed by a consortium of laboratories in the Rosetta Commons, has an unmatched variety of functionalities and is one of the most accurate protein structure prediction and design approaches. The workshops teach how to measure and manipulate protein conformations, calculate energies in low- and high-resolution representations, fold proteins from sequence, model variable regions of proteins (loops), dock proteins or small molecules, design protein sequences, and build custom protocols for operations tailored to particular biomolecular applications.
Book Synopsis Prediction of Contact Maps Using Support Vector Machines by :
Download or read book Prediction of Contact Maps Using Support Vector Machines written by and published by . This book was released on 2002 with total page 13 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contact map prediction is of great interests for its application in fold recognition and protein 3D structure determination. In particular, we focusd on predicting non-local interactions in this paper. We employed Support Vector Machines (SVMs) as the machine learning tool and incorporated AAindex to extract correlated mutation analysis (CMA) and sequence profile (SP) features. In addition, we evaluated the effectiveness of different features for various fold classes. On average, our predictor achieved an prediction accuracy of 0.2238 with an improvement over a randompredictor of a factor 11.7, which is better than reported studies. Our study showed that predicted secondary structure features play an important roles for the proteins containing beta structures. Models based on secondary structure features and CMA features produce different sets of predictions. Our study also suggests that models learned separately for different protein fold families may achieve better performance than a unified model.
Book Synopsis Information and Communication Technology by : Durgesh Kumar Mishra
Download or read book Information and Communication Technology written by Durgesh Kumar Mishra and published by Springer. This book was released on 2017-10-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book volume contains 31 papers presented at ICICT 2016: Second International Congress on Information and Communication Technology. The conference was held during 12-13 December 2016, Bangkok, Thailand and organized communally by G R Foundation, and Computer Society of India Division IV – Communication and Division V – Education and Research. This volume contains papers mainly focused on ICT for computation, algorithms and data analytics, and IT security.
Book Synopsis The Resolution Revolution: Recent Advances In cryoEM by :
Download or read book The Resolution Revolution: Recent Advances In cryoEM written by and published by Academic Press. This book was released on 2016-08-26 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: cryoEM, a new volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods and new developments in recording images, the creation, evaluation and validation of 3D maps from the images, model building into maps and refinement of the resulting atomic structures, and applications of essentially single particle methods to helical structures and to sub-tomogram averaging. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods that determine the structures of biological molecules, a vital step for understanding their function Contains the technical developments underpinning the advances of cryoEM and captures the exciting insights that have resulted
Book Synopsis Let the Evidence Speak by : Alan Jessop
Download or read book Let the Evidence Speak written by Alan Jessop and published by Springer. This book was released on 2018-05-31 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the most important ideas behind Bayes’ Rule in a form suitable for the general reader. It is written without formulae because they are not necessary; the ability to add and multiply is all that is needed. As well as showing in full the application of Bayes’ Rule to some quantitatively simple, though not trivial, examples, the book also convincingly demonstrates that some familiarity with Bayes’ Rule is helpful in thinking about how best to structure one’s thinking.
Book Synopsis Machine Learning Meets Quantum Physics by : Kristof T. Schütt
Download or read book Machine Learning Meets Quantum Physics written by Kristof T. Schütt and published by Springer Nature. This book was released on 2020-06-03 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.
Book Synopsis Coarse-Grained Modeling of Biomolecules by : Garegin A. Papoian
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
