Novel Methods in Computational Analysis and Design of Protein-protein Interactions - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Novel Methods in Computational Analysis and Design of Protein-protein Interactions write by Brian Alan Joughin. This book was released on 2007. Novel Methods in Computational Analysis and Design of Protein-protein Interactions available in PDF, EPUB and Kindle. This thesis presents a number of novel computational methods for the analysis and design of protein-protein complexes, and their application to the study of the interactions of phosphopeptides with phosphopeptide-binding domain interactions. A novel protein-protein interaction type, the action-at-a-distance interaction, is described in the complex of the TEM1 P-lactamase with the 3-lactamase inhibitor protein (BLIP). New action-at-a-distance interactions were designed on the surface of BLIP and computed to enhance the affinity of that complex. A new method is described for the characterization and prediction of protein ligand-binding sites. This method was used to analyze the phosphoresidue-contacting sites of known phosphopeptide-binding domains, and to predict the sites of phosphoresidue-contact on some protein domains for which the correct site was not known. The design of a library of variant WW domains that is predicted to be enriched in domains that might have specificity for "pS/pT-Q" peptide ligands is detailed. General methods for designing libraries of degenerate oligonucleotides for expressing protein libraries as accurately as possible are given, and applied to the described WW domain variant library.
Protein Interactions: Computational Methods, Analysis And Applications
Protein Interactions: Computational Methods, Analysis And Applications - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Protein Interactions: Computational Methods, Analysis And Applications write by M Michael Gromiha. This book was released on 2020-03-05. Protein Interactions: Computational Methods, Analysis And Applications available in PDF, EPUB and Kindle. This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Computational Analysis of Protein-protein Interactions
Computational Analysis of Protein-protein Interactions - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Computational Analysis of Protein-protein Interactions write by Sam Ansari. This book was released on 2007. Computational Analysis of Protein-protein Interactions available in PDF, EPUB and Kindle.
Protein-Protein Interaction Networks
Protein-Protein Interaction Networks - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Protein-Protein Interaction Networks write by Stefan Canzar. This book was released on 2019-10-04. Protein-Protein Interaction Networks available in PDF, EPUB and Kindle. This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.
Protein Interaction Networks
Protein Interaction Networks - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Protein Interaction Networks write by Aidong Zhang. This book was released on 2009-04-06. Protein Interaction Networks available in PDF, EPUB and Kindle. The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.
