Title Homology modeling : methods and protocols / edited by Andrew J.W. Orry, Ruben Abagyan

Published New York : Humana Press, ©2012

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Description 1 online resource (xi, 419 pages) Series Methods in molecular biology, 1064-3745 ; 857 Methods in molecular biology ; 857. Contents Classification of proteins : available structural space for molecular modeling / Antonina Andreeva -- Effective techniques for protein structure mining / Stefan J. Suhrer [and others] -- Methods for sequence-structure alignment / Ceslovas Venclovas -- Force fields for homology modeling / Andrew J. Bordner -- Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal / Lorenza Bordoli and Torsten Schwede -- Practical introduction to molecular dynamics simulations : applications to homology modeling / Alessandra Nurisso, Antoine Daina, and Ross C. Walker -- Methods for accurate homology modeling by global optimization / Keehyoung Joo, Jinwoo Lee, and Jooyoung Lee -- Ligand-guided receptor optimization / Vsevolod Katritch, Manuel Rueda, and Ruben Abagyan -- Loop simulations / Maxim Totrov -- Methods of protein structure comparison / Irina Kufareva and Ruben Abagyan -- Homology modeling of class A G protein-coupled receptors / Stefano Costanzi -- Homology modeling of transporter proteins (carriers and ion channels) / Aina Westrheim Ravna and Ingebrigt Sylte -- Methods for the homology modeling of antibody variable regions / Aroop Sircar -- Investigating protein variants using structural calculation techniques / Jonas Carlsson and Bengt Persson -- Macromolecular assembly structures by comparative modeling and electron microscopy / Keren Lasker [and others] -- Preparation and refinement of model protein-ligand complexes / Andrew J.W. Orry and Ruben Abagyan -- Modeling peptide-protein interactions / Nir London, Barak Raveh, and Ora Schueler-Furman -- Comparison of common homology modeling algorithms : application of user-defined alignments / Michael A. Dolan, James W. Noah, and Darrell Hurt Summary Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure. In, Homology Modeling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Homology Modeling: Methods and Protocols guides scientists in the available homology modeling methods Analysis Life sciences Biochemistry Protein Science Protein Structure eiwitten proteins moleculaire biologie molecular biology modelleren modeling protocollen protocols methodologie methodology Proteins and Enzymes Eiwitten en enzymen Notes Includes index Bibliography Includes bibliographical references and index Notes English Subject Sequence alignment (Bioinformatics) Mathematical models. Structure-activity relationships (Biochemistry) Amino acids. Sequence Homology Models, Theoretical Biochemical Phenomena Pharmacological Phenomena Amino Acids, Peptides, and Proteins Investigative Techniques Chemicals and Drugs Genetic Phenomena Physiological Phenomena Chemical Phenomena Analytical, Diagnostic and Therapeutic Techniques and Equipment Phenomena and Processes Models, Molecular Structure-Activity Relationship Sequence Homology, Amino Acid Amino Acids Sequence Alignment mathematical models. Structure-activity relationships (Biochemistry) Mathematical models Amino acids Sequence alignment (Bioinformatics) Genre/Form Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Orry, Andrew J. W Abagyan, Ruben ISBN 9781617795886 1617795887 1617795879 9781617795879

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