UID:
almahu_9949388155502882
Format:
1 online resource (xiv, 377 pages .)
ISBN:
9781788012560
,
1788012569
,
9781788010139
,
1788010132
Series Statement:
Chemical biology ; no. 3
Content:
This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.
Note:
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 Servers1.4 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 Modelling2.2.3 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 Chemistry3.1 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 Method4.2.2 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
Additional Edition:
Print version: Computational tools for chemical biology. London, UK : Royal Society of Chemistry, [2018] ISBN 1782627006
Additional Edition:
ISBN 9781782627005
Language:
English
Keywords:
Electronic books.
URL:
https://doi.org/10.1039/9781788010139
