Computational Tools for Chemical Biology
The rapid development of efficient computational tools has allowed researchers to tackle biological problems and to predict, analyse and monitor, at an atomic level, molecular recognition processes. This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.
Chapters from internationally renowned leaders in the field introduce concepts and discuss the impact of technological advances in computer hardware and software in explaining and predicting phenomena involving biomolecules, from small molecules to macromolecular systems. Important topics from the understanding of biomolecules to the modification of their functions are addressed, as well as examples of the application of tools in drug discovery, glycobiology, protein design and molecular recognition. Not only are the cutting-the-edge methods addressed, but also their limitations and possible future development.
For anyone wishing to learn how computational chemistry and molecular modelling can provide information not easily accessible through other experimental methods, this book will be a valuable resource. It will be of interest to postgraduates and researchers in the biological and chemical sciences, medicinal and pharmaceutical chemistry, and theoretical chemistry.
Computational Tools for Chemical Biology, The Royal Society of Chemistry, 2017.
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Table of contents
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Chapter 1: Computational Chemistry and Molecular Modelling Basicsp1-38BySamuel Genheden;Samuel GenhedenDepartment of Chemistry and Molecular Biology, University of Gothenburg405 30 GöteborgSweden[email protected]Search for other works by this author on:Anna Reymer;Anna ReymerDepartment of Chemistry and Molecular Biology, University of Gothenburg405 30 GöteborgSweden[email protected]Search for other works by this author on:Patricia Saenz-Méndez;Patricia Saenz-MéndezDepartment of Chemistry and Molecular Biology, University of Gothenburg405 30 GöteborgSweden[email protected]Computational Chemistry and Biology Group, Facultad de QuímicaUdelaR, 11800 MontevideoUruguaySearch for other works by this author on:Leif A. ErikssonLeif A. ErikssonDepartment of Chemistry and Molecular Biology, University of Gothenburg405 30 GöteborgSweden[email protected]Search for other works by this author on:
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Chapter 2: Molecular Dynamics Computer Simulations of Biological Systemsp39-68ByFernando BresmeFernando BresmeSearch for other works by this author on:
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Chapter 3: Designing Chemical Tools with Computational Chemistryp69-86BySilvia Rinaldi;Silvia RinaldiIstituto di Chimica del Riconoscimento MolecolareCNR, Via Mario Bianco 920131 MilanoItaly[email protected]Search for other works by this author on:Giorgio ColomboGiorgio ColomboIstituto di Chimica del Riconoscimento MolecolareCNR, Via Mario Bianco 920131 MilanoItaly[email protected]Search for other works by this author on:
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Chapter 4: Computational Design of Protein Functionp87-107ByMarc Garcia-Borràs;Marc Garcia-BorràsDepartment of Chemistry and Biochemistry, University of CaliforniaLos AngelesCalifornia CA 90095-1569USASearch for other works by this author on:Kendall N. Houk;Kendall N. HoukDepartment of Chemistry and Biochemistry, University of CaliforniaLos AngelesCalifornia CA 90095-1569USASearch for other works by this author on:Gonzalo Jiménez-OsésGonzalo Jiménez-OsésDepartamento de Química, Centro de Investigación en Síntesis QuímicaUniversidad de La Rioja26006 LogroñoLa RiojaSpain[email protected]Search for other works by this author on:
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Chapter 5: Computational Enzymology: Modelling Biological Catalystsp108-144ByLaura Masgrau;Laura MasgrauInstitut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpain[email protected][email protected]Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpainSearch for other works by this author on:Àngels González-Lafont;Àngels González-LafontInstitut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpain[email protected][email protected]Departament de Química, Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpainSearch for other works by this author on:José M. LluchJosé M. LluchInstitut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpain[email protected][email protected]Departament de Química, Universitat Autònoma de Barcelona08193 Bellaterra (Cerdanyola del Vallès), BarcelonaSpainSearch for other works by this author on:
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Chapter 6: Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactionsp145-164ByAlessandra Nurisso;Alessandra NurissoSchool of Pharmaceutical SciencesUniversity of Geneva, University of Lausanne, Rue Michel Servet 1CH-1211 Geneva 4SwitzerlandSearch for other works by this author on:Jesús Jiménez-Barbero;Jesús Jiménez-BarberoCIC-bioGUNE, Bizkaia Science and Technology Park48160-DerioSpainSearch for other works by this author on:Sonsoles Martín-SantamaríaSonsoles Martín-SantamaríaSearch for other works by this author on:
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Chapter 7: Molecular Modelling of Nucleic Acidsp165-197ByHansel Gómez;Hansel GómezInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainSearch for other works by this author on:Jürgen Walther;Jürgen WaltherInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainSearch for other works by this author on:Leonardo Darré;Leonardo DarréInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainSearch for other works by this author on:Ivan Ivani;Ivan IvaniInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainSearch for other works by this author on:Pablo D. Dans;Pablo D. DansInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainSearch for other works by this author on:Modesto OrozcoModesto OrozcoInstitute for Research in Biomedicine (IRB Barcelona) – The Barcelona Institute of Science and Technology08028 BarcelonaSpain[email protected]Joint BSC-CRG-IRB Program in Computational Biology, Institute for Research in BiomedicineBarcelonaSpainDepartment of Biochemistry and Molecular BiomedicineFaculty of Biology, University of Barcelona, 08028 BarcelonaSpainSearch for other works by this author on:
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Chapter 8: Uncovering GPCR and G Protein Function by Protein Structure Network Analysisp198-220ByFrancesca Fanelli;Francesca FanelliCenter for Neuroscience and NeurotechnologyUniversity of Modena and Reggio EmiliaItalySearch for other works by this author on:Angelo FellineAngelo FellineSearch for other works by this author on:
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Chapter 9: Current Challenges in the Computational Modelling of Molecular Recognition Processesp221-246BySonsoles Martín-SantamaríaSonsoles Martín-SantamaríaSearch for other works by this author on:
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Chapter 10: Novel Insights into Membrane Transport from Computational Methodologiesp247-280ByVictoria Oakes;Victoria OakesDepartment of Chemistry, Britannia House, 7 Trinity Street, King's College LondonLondon SE1 1DBUK[email protected]Search for other works by this author on:Carmen DomeneCarmen DomeneDepartment of Chemistry, Britannia House, 7 Trinity Street, King's College LondonLondon SE1 1DBUK[email protected]Chemistry Research Laboratory, Mansfield Road, University of OxfordOxford OX1 3TAUKSearch for other works by this author on:
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Chapter 11: Application of Molecular Modelling to Speed-up the Lead Discovery Processp281-316ByIuni M. L. Trist;Iuni M. L. TristUniversità degli Studi di Siena, Dipartimento di Biotecnologie Chimica e FarmaciaVia A. Moro 2Siena53100Italy[email protected]Search for other works by this author on:Maurizio Botta;Maurizio BottaUniversità degli Studi di Siena, Dipartimento di Biotecnologie Chimica e FarmaciaVia A. Moro 2Siena53100Italy[email protected]Sbarro Institute for Cancer Research and Molecular Medicine, Center of Biotechnology, College of Science and Technology, Temple UniversityBioLife, Science Bldg., Suite 333, 1900 N 12th StreetPhiladelphiaPA19122USASearch for other works by this author on:Anna Lucia FallacaraAnna Lucia FallacaraUniversità degli Studi di Siena, Dipartimento di Biotecnologie Chimica e FarmaciaVia A. Moro 2Siena53100Italy[email protected]Search for other works by this author on:
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Chapter 12: Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targetsp317-348ByMarco De Vivo;Marco De VivoLaboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di TecnologiaVia Morego 3016163 GenoaItaly[email protected]IAS-S/INM-9 Computational Biomedicine Forschungszentrum JülichWilhelm-Johnen-Staßig;e 52428 JülichGermany[email protected]Search for other works by this author on:Matteo Masetti;Matteo MasettiDepartment of Pharmacy & Biotechnology, Alma Mater Studiorum, University of BolognaVia Belmeloro 640126 BolognaItaly[email protected]Search for other works by this author on:Giulia RossettiGiulia RossettiIAS-S/INM-9 Computational Biomedicine Forschungszentrum JülichWilhelm-Johnen-Staßig;e 52428 JülichGermany[email protected]Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen UniversityPauwelsstraßig;e 3052074 AachenGermanyJülich Supercomputing Centre (JSC) – Division Computational Science – Simulation Laboratory Biology, Forschungszentrum Jülich52425 JülichGermanySearch for other works by this author on:
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Chapter 13: The Polypharmacology Gap Between Chemical Biology and Drug Discoveryp349-370ByAlbert A. Antolin;Albert A. AntolinResearch Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu FabraDoctor Aiguader 8808003 Barcelona, CataloniaSpain[email protected]Search for other works by this author on:Jordi MestresJordi MestresResearch Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu FabraDoctor Aiguader 8808003 Barcelona, CataloniaSpain[email protected]Search for other works by this author on:
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