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RSC Biomolecular Sciences
Innovations in Biomolecular Modeling and Simulations
Edited by
Tamar Schlick
Tamar Schlick
New York University, USA
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Volume
2
Hardback ISBN:
978-1-84973-462-2
PDF ISBN:
978-1-84973-505-6
No. of Pages:
354
Publication date:
01 May 2012
About this book
The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Innovations in Biomolecular Modeling and Simulations, The Royal Society of Chemistry, 2012.
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Digital access
$216.00
Print format
Innovations in Biomolecular Modeling and Simulations
$216.00
Table of contents
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Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scalep3-32ByFilip LankašFilip LankašCentre for Complex Molecular Systems and BiomoleculesInstitute of Organic Chemistry and BiochemistryAcademy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6Czech Republic[email protected]Search for other works by this author on:
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Chapter 2: Molecular Dynamics and Force Field Based Methods for Studying Quadruplex Nucleic Acidsp33-52ByShozeb M Haider;Shozeb M HaiderCentre for Cancer Research and Cell BiologyQueen's University Belfast97 Lisburn Road, Belfast BT9 7BLUKSearch for other works by this author on:Stephen NeidleStephen NeidleCenter for Cancer MedicinesThe School of Pharmacy, University of LondonLondon WC1N 1AXUK[email protected]Search for other works by this author on:
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Chapter 3: Opposites Attract: Shape and Electrostatic Complementarity in Protein-DNA Complexesp53-80ByRobert C. Harris;Robert C. HarrisDepartment of Physics andInstitute of Molecular BiophysicsFlorida State UniversityTallahassee, FL 32306USASearch for other works by this author on:Travis Mackoy;Travis MackoyInstitute of Molecular BiophysicsFlorida State UniversityTallahassee, FL 32306USASearch for other works by this author on:Ana Carolina Dantas Machado;Ana Carolina Dantas MachadoMolecular and Computational Biology Program, Departments of Biological Sciences and ChemistryUniversity of Southern California1050 Childs Way, Los Angeles, CA 90089USASearch for other works by this author on:Darui Xu;Darui XuInstitute of Molecular BiophysicsFlorida State UniversityTallahassee, FL 32306USADepartment of PharmacologyUniversity of Texas Southwestern Medical CenterDallas, TX 75390USA[email protected]; [email protected]Search for other works by this author on:Remo Rohs;Remo RohsMolecular and Computational Biology Program, Departments of Biological Sciences and ChemistryUniversity of Southern California1050 Childs Way, Los Angeles, CA 90089USASearch for other works by this author on:Marcia Oliveira FenleyMarcia Oliveira FenleyInstitute of Molecular BiophysicsFlorida State UniversityTallahassee, FL 32306USASearch for other works by this author on:
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Chapter 4: Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanismp81-110ByMeredith C. Foley;Meredith C. FoleyDepartment of Chemistry and Courant Institute of Mathematical SciencesNew York University251 Mercer Street, New YorkNew York 10012, USASearch for other works by this author on:Karunesh Arora;Karunesh AroraDepartment of Chemistry & Biophysics ProgramUniversity of Michigan, Ann ArborMI 48109USA[email protected]Search for other works by this author on:Tamar SchlickTamar SchlickDepartment of Chemistry and Courant Institute of Mathematical SciencesNew York University251 Mercer Street, New YorkNew York 10012, USASearch for other works by this author on:
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Chapter 5: Molecular Dynamics Structure Prediction of a Novel Protein–DNA Complex: Two HU Proteins with a DNA Four-way Junctionp111-128ByElizabeth G. Wheatley;Elizabeth G. WheatleyDepartments of ChemistryMolecular Biology and Biochemistry, and Molecular Biophysics Program,Wesleyan University06459Middletown, CTUSA[email protected]; [email protected]Search for other works by this author on:Susan N. Pieniazek;Susan N. PieniazekDepartments of ChemistryMolecular Biology and Biochemistry, and Molecular Biophysics Program,Wesleyan University06459Middletown, CTUSA[email protected]; [email protected]Search for other works by this author on:Iulia Vitoc;Iulia VitocDepartments of ChemistryMolecular Biology and Biochemistry, and Molecular Biophysics Program,Wesleyan University06459Middletown, CTUSA[email protected]; [email protected]Search for other works by this author on:Ishita Mukerji;Ishita MukerjiDepartments of ChemistryMolecular Biology and Biochemistry, and Molecular Biophysics Program,Wesleyan University06459Middletown, CTUSA[email protected]; [email protected]Search for other works by this author on:D.L. BeveridgeD.L. BeveridgeDepartments of ChemistryMolecular Biology and Biochemistry, and Molecular Biophysics Program,Wesleyan University06459Middletown, CTUSA[email protected]; [email protected]Search for other works by this author on:
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Chapter 6: Molecular Dynamics Simulations of RNA Moleculesp129-155ByJ. Šponer;J. ŠponerInstitute of BiophysicsAcademy of Sciences of the Czech RepublicKrálovopolská 135, 612 65 BrnoCzech RepublicSearch for other works by this author on:M. Otyepka;M. OtyepkaRegional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of SciencePalacky UniversityOlomouc, Tr. 17. Listopadu 12, 771 46 OlomoucCzech RepublicSearch for other works by this author on:P. Banáš;P. BanášRegional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of SciencePalacky UniversityOlomouc, Tr. 17. Listopadu 12, 771 46 OlomoucCzech RepublicSearch for other works by this author on:K. Réblová;K. RéblováInstitute of BiophysicsAcademy of Sciences of the Czech RepublicKrálovopolská 135, 612 65 BrnoCzech RepublicSearch for other works by this author on:N. G. WalterN. G. WalterDepartment of Chemistry, Single Molecule Analysis GroupUniversity of Michigan930 N. University Ave., Ann Arbor, MI 48109-1055USA[email protected]Search for other works by this author on:
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Chapter 7: The Structure and Folding of Helical Junctions in RNAp156-176ByDavid M. J. LilleyDavid M. J. LilleyCancer Research UK Nucleic Acid Structure Research Group, MSI/WTB ComplexThe University of DundeeDow Street, Dundee DD1 5EHU.K.[email protected]Search for other works by this author on:
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Chapter 8: Structure and Dynamics of Supercoiled DNA Knots and Catenanesp179-197ByGuillaume Witz;Guillaume WitzEcole Polytechnique Fédérale de LausanneLaboratoire de Physique de la Matière Vivante1015 LausanneSwitzerlandSearch for other works by this author on:Andrzej StasiakAndrzej StasiakSearch for other works by this author on:
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Chapter 9: Monte Carlo Simulations of Nucleosome Chains to Identify Factors that Control DNA Compaction and Accessp198-235ByKarsten Rippe;Karsten RippeDeutsches Krebsforschungszentrum (DKFZ) & BioQuantResearch Group Genome Organization & FunctionIm Neuenheimer Feld 280, 69120 HeidelbergGermany[email protected]Search for other works by this author on:Rene Stehr;Rene StehrUniversity of Applied Sciences StralsundCC BioinformaticsZur Schwedenschanze 15, 18435 StralsundGermany[email protected]; [email protected]Search for other works by this author on:Gero WedemannGero WedemannUniversity of Applied Sciences StralsundCC BioinformaticsZur Schwedenschanze 15, 18435 StralsundGermany[email protected]; [email protected]Search for other works by this author on:
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Chapter 10: Sliding Dynamics Along DNA: A Molecular Perspectivep236-262ByYaakov LevyYaakov LevySearch for other works by this author on:
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Chapter 11: Structure-based Design Technology CONTOUR and its Application to Drug Discoveryp265-280BySuresh B. SinghSuresh B. SinghSearch for other works by this author on:
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Chapter 12: Molecular Simulation in Computer-aided Drug Design: Algorithms and Applicationsp281-315ByRobert V. Swift;Robert V. SwiftDepartment of Chemistry and BiochemistryUniversity of CaliforniaSan Diego, La Jolla, CA 92093-0340USA[email protected]Search for other works by this author on:Rommie E. AmaroRommie E. AmaroDepartment of Chemistry and BiochemistryUniversity of CaliforniaSan Diego, La Jolla, CA 92093-0340USA[email protected]Search for other works by this author on:
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Chapter 13: Computer-aided Drug Discovery: Two Antiviral Drugs for HIV/AIDSp316-319ByJ. Andrew McCammonJ. Andrew McCammonHoward Hughes Medical Institute, NSF Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of PharmacologyUniversity of California at San DiegoLa Jolla, CA92093-0365USA[email protected]Search for other works by this author on:
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