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Computational tools for chemical biology

Author: Sonsoles Martin-Santamaria
Publisher: London, UK : Royal Society of Chemistry, [2018]
Series: Chemical biology series, no. 3.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:
This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.
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Genre/Form: Electronic books
Additional Physical Format: (OCoLC)968162319
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Sonsoles Martin-Santamaria
ISBN: 9781788012560 1788012569 9781788010139 1788010132
OCLC Number: 1015233395
Description: 1 online resource (xiv, 377 pages.)
Contents: ""Title""; ""Copyright""; ""Contents""; ""Chapter 1 Computational Chemistry and Molecular Modelling Basics""; ""1.1 Introduction""; ""1.2 Techniques in Biomolecular Simulations""; ""1.2.1 Molecular Mechanics and Force Fields""; ""1.2.2 Basic Simulation Techniques""; ""1.2.3 Basic Data Analysis""; ""1.2.4 Software""; ""1.2.5 Examples""; ""1.3 Protein Structure Prediction""; ""1.3.1 Sequence Alignment and Secondary Structure Prediction""; ""1.3.2 Comparative Modelling Approaches""; ""1.3.3 Function Prediction""; ""1.3.4 Analysing the Quality of the Modelled Structure"" ""1.3.5 Software and Web Based Servers""""1.4 Computer-based Drug Design""; ""1.4.1 Pre-requisites for SBDDâ#x80;#x94;Sampling Algorithms and Scoring Functions""; ""1.4.2 Structure Based Drug Design (SBDD)""; ""1.4.3 Ligand Based Drug Design (LBDD)""; ""1.4.4 Pharmacophores""; ""1.4.5 Compound Optimisation""; ""1.4.6 Software and Web Based Servers""; ""Acknowledgements""; ""References""; ""Chapter 2 Molecular Dynamics Computer Simulations of Biological Systems""; ""2.1 Introduction""; ""2.2 The Basics of Molecular Dynamics""; ""2.2.1 Force Fields for Biomolecular Simulations"" ""2.2.2 Multiscale Modelling""""2.2.3 Advanced Force Fields""; ""2.3 Extracting the Information from MD""; ""2.3.1 Free Energy Difference Between Two States""; ""2.3.2 Enhanced Configurational Sampling""; ""2.3.3 Simulating Rare Events""; ""2.3.4 Computing Elastic Properties in Biomolecular Simulations""; ""2.4 MD Simulation vs. Experiment""; ""2.4.1 NMR and MD: Structure and Dynamics""; ""2.4.2 Structure of Biomolecules and Diffraction: Solving the Phase Problem with MD""; ""2.5 Future Directions""; ""2.6 Conclusion""; ""Acknowledgements""; ""References"" ""Chapter 3 Designing Chemical Tools with Computational Chemistry""""3.1 Introduction""; ""3.2 Structure Based Approaches for Chemical Biology""; ""3.3 Structural Dynamics as a Source of Novel Chemical Tools""; ""3.4 Combining Bioinformatics, Chemoinformatics and Structural Information to Explore Protein Functions""; ""3.5 Deep Networks and Big Data in the Discovery of New Drugs and Chemical Tools""; ""3.6 Conclusions and Perspectives""; ""References""; ""Chapter 4 Computational Design of Protein Function""; ""4.1 Introduction""; ""4.2 The â#x80;#x98;Inside-outâ#x80;#x99; Design Protocol"" ""4.2.1 Description of the Method""""4.2.2 Enzymes Designed Though the â#x80;#x98;Inside-outâ#x80;#x99; Approach: Kemp Eliminases""; ""4.3 QM/MM Approaches to Enzyme Design""; ""4.3.1 Description of the Methods""; ""4.3.2 Engineered Butyrylcholinesterase for Cocaine Detoxification""; ""4.3.3 Electron Transfer Reactions Catalysed by Metalloproteins""; ""4.4 Summary and Outlook""; ""Acknowledgements""; ""References""; ""Chapter 5 Computational Enzymology: Modelling Biological Catalysts""; ""5.1 Introduction""; ""5.2 General Framework""; ""5.2.1 The Transition State and the Energy Barrier""
Series Title: Chemical biology series, no. 3.
Responsibility: edited by Sonsoles Martín-Santamaría.

Abstract:

This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.  Read more...

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