Verfügbarkeit: Solvation of protein binding sites and optimisation of protein-protein complex prediction

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Bibliographische Detailangaben
Titel:	Solvation of protein binding sites and optimisation of protein-protein complex prediction
Von:	Sebastian Eckehart Schneider
Person:	Schneider, Sebastian Eckehart Verfasser aut
Hauptverfasser:	Schneider, Sebastian Eckehart (VerfasserIn)
Format:	Abschlussarbeit Buch
Sprache:	Englisch
Veröffentlicht:	2012
Schlagworte:	Bindestelle Proteine Lösungsmittel Hochschulschrift
Online-Zugang:	http://mediatum.ub.tum.de/node?id=1106907 https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20120712-1106907-1-6 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025374042&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
Beschreibung:	166 S. graph. Darst.

Internformat

MARC


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Datensatz im Suchindex

DE-BY-OTHR_katkey	5033643
DE-BY-TUM_call_number	0001 DM 30229
DE-BY-TUM_katkey	1891614
DE-BY-TUM_location	Mag
DE-BY-TUM_media_number	TEMP3214667
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adam_text	IMAGE 1 CONTENTS 1 INTRODUCTION 1 2 FUNDAMENTALS 3 2.1 PROTEIN INTERACTIONS 3 2.2 PROTEIN INTERACTION PREDICTION 7 2.2.1 PROTEIN-PROTEIN INTERACTION PREDICTION 7 2.2.2 PROTEIN-SMALL LIGAND INTERACTION PREDICTION 11 2.3 PROTEIN-PROTEIN DOCKING 16 2.3.1 RIGID PROTEIN-PROTEIN DOCKING METHODS 16 2.3.2 FLEXIBLE PROTEIN-PROTEIN DOCKING METHODS 19 2.3.3 THE ATTRACT DOCKING PROGRAM 22 2.3.4 APPLICATION OF PROTEIN-PROTEIN BINDING SITE PREDICTION IN PROTEIN-PROTEIN DOCKING 23 2.4 MOLECULAR DYNAMICS SIMULATIONS 24 2.4.1 MOLECULAR DYNAMICS SIMULATION STEPS AND ALGORITHMS . . 24 2.4.2 SOLVATION OF BIOMOLECULES 26 2.5 MOTIVATION 30 2.5.1 ACKNOWLEDGMENT 33 3 SOLVATION O F PROTEINS IN EXPLICIT SOLVENT SIMULATIONS 35 3.1 MOLECULAR DYNAMICS SIMULATIONS OF PROTEINS: SETTING AND APPLI CATION 37 3.1.1 SIMULATIONS IN AQUEOUS SOLVENTS 37 3.1.2 MOLECULAR DYNAMICS SIMULATION PROTOCOL . . 39 3.1.3 TEST SETS 40 3.2 SOLVENT PROFILES ON THE PROTEINS SURFACES 41 HTTP://D-NB.INFO/1029691061 IMAGE 2 3.2.1 MEASUREMENT OF THE RADIAL SOLVENT DISTRIBUTION AROUND PROTEINS 42 3.2.2 ORIENTATION AND DENSITY DISTRIBUTION OF ISOPROPYL ALCOHOL MOLECULES AT THE SURFACE 44 3.2.3 SOLVENT-SOLUTE CONTACT TIME 46 3.2.4 GRID BASED SAMPLING PRINCIPLES AND SAMPLING ISSUES . . . 48 3.2.5 GIBBS FREE ENERGY APPROXIMATION FROM RIGID GRID CALCU LATIONS 51 3.2.6 SOLVATION PROFILES FOR IPROH 53 3.3 SOLVATION OF BINDING SITES 57 3.3.1 WATER IN PROTEIN-PROTEIN BINDING SITES 57 3.3.2 BINDING SITE SOLVATION USING A MIXED SOLVENT 61 3.4 CONCLUSION 71 3.4.1 ACKNOWLEDGMENT 73 4 DESOLVATION PROPERTIES O F SMALL LIGAND BINDING SITES 75 4.1 SETTINGS AND STATISTICAL MEASUREMENTS 77 4.1.1 STRUCTURE PREPARATION AND PREREQUISITES 77 4.1.2 STATISTICAL MEASUREMENTS 78 4.1.3 EVALUATION OF PREDICTION QUALITY 79 4.2 GEOMETRY-BASED CAVITY DETECTION 80 4.2.1 PRINCIPLES OF THE CAVITY DETECTION ALGORITHM 80 4.2.2 PERFORMANCE OF INITIAL CAVITY DETECTION 81 4.3 ENERGY CALCULATION PROCEDURE AND STATISTICS 85 4.3.1 CALCULATION OF DESOLVATION PROPERTIES IN CAVITIES 85 4.3.2 DESOLVATION FREE ENERGY STATISTICS AND GENERALIZED BORN SETTINGS 86 4.4 PREDICTING BINDING SITE GEOMETRIES USING DESOLVATION PENALTIES . . 88 4.4.1 CLUSTERING OF DESOLVATION PENALTIES 88 4.4.2 PERFORMANCE OF THE BINDING SITE PREDICTION 90 4.5 CONCLUSION 95 5 OPTIMIZING UNBOUND PROTEIN-PROTEIN DOCKING 9 7 5.1 SETTINGS AND PROCEEDINGS 99 IMAGE 3 5.1.1 BINDING SITE PREDICTION, BENCHMARK SET AND ACCEPTANCE CRITERIA 99 5.1.2 FORCEFIELD PERFORMANCE ON THE UNBOUND TEST SET 100 5.2 DOCKING PERFORMANCE EVALUATION USING ARTIFICIAL BINDING SITES . . 101 5.2.1 CREATION OF ARTIFICIAL BINDING SITES FOR KNOWN BINDING SITE DOCKING 101 5.2.2 DOCKING WITH KNOWN BINDING SITES 101 5.2.3 VARIATIONS OF BINDING SITES COVERING POSSIBLE BINDING SITE PREDICTION MOTIFS 104 5.3 SINGLE AND MULTIPLE RESIDUE EXPERIMENTS 105 5.3.1 INCLUSION OF KNOWLEDGE ON SINGLE RESIDUES 107 5.4 HANDLING INFORMATION FROM PROTEIN-PROTEIN BINDING SITE PREDICTIONS 108 5.4.1 INCLUSION OF PREDICTIONS ON PROTEIN-PROTEIN INTERACTION RE GIONS 108 5.5 FLEXIBLE DOCKING USING NORMAL MODE RELAXATION 113 5.6 BINDING SITE PREDICTION USING TOP RANKED DOCKING RESULTS 117 5.6.1 BINDING SITE PREDICTION USING THE ATTRACT SCORE . . .117 5.6.2 WEIGHTED DOCKING USING ATTRACT SCORE AS PREDICTOR . . 119 5.7 CONCLUSION 122 5.7.1 ACKNOWLEDGMENT 123 6 PREDICTION O F T H E ANTIBODY FC INTERACTION WITH T H E C L Q COM PONENT 125 6.1 THE CLQ-IGGL COMPLEX 126 6.1.1 FUNCTION OF THE CLQ-ANTIBODY-FC BINDING IN THE COMPLE MENT SYSTEM 126 6.1.2 RESIDUES INVOLVED IN CLQ-ANTIBODY-FC BINDING 128 6.2 COMPUTER-AIDED ALL ATOM COMPLEX PREDICTION 130 6.2.1 DOCKING AND REFINEMENT SCHEME 130 6.2.2 CL-IGGL COMPLEX PREDICTION 131 6.3 IDENTIFICATION OF SURFACE RESIDUES THAT MEDIATE THE INTERACTION . . 134 6.4 CONCLUSION 138 6.4.1 ACKNOWLEDGMENT 139 IMAGE 4 7 CONCLUSION AND OUTLOOK 141 7.1 CONCLUSION 141 7.2 OUTLOOK AND FUTURE WORK 143 A LIST O F PUBLICATIONS 147
any_adam_object	1
author	Schneider, Sebastian Eckehart
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discipline	Chemie / Pharmazie Biologie
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spellingShingle	Schneider, Sebastian Eckehart Solvation of protein binding sites and optimisation of protein-protein complex prediction Bindestelle (DE-588)4145563-0 gnd Proteine (DE-588)4076388-2 gnd Lösungsmittel (DE-588)4036160-3 gnd
subject_GND	(DE-588)4145563-0 (DE-588)4076388-2 (DE-588)4036160-3 (DE-588)4113937-9
title	Solvation of protein binding sites and optimisation of protein-protein complex prediction
title_auth	Solvation of protein binding sites and optimisation of protein-protein complex prediction
title_exact_search	Solvation of protein binding sites and optimisation of protein-protein complex prediction
title_full	Solvation of protein binding sites and optimisation of protein-protein complex prediction Sebastian Eckehart Schneider
title_fullStr	Solvation of protein binding sites and optimisation of protein-protein complex prediction Sebastian Eckehart Schneider
title_full_unstemmed	Solvation of protein binding sites and optimisation of protein-protein complex prediction Sebastian Eckehart Schneider
title_short	Solvation of protein binding sites and optimisation of protein-protein complex prediction
title_sort	solvation of protein binding sites and optimisation of protein protein complex prediction
topic	Bindestelle (DE-588)4145563-0 gnd Proteine (DE-588)4076388-2 gnd Lösungsmittel (DE-588)4036160-3 gnd
topic_facet	Bindestelle Proteine Lösungsmittel Hochschulschrift
url	http://mediatum.ub.tum.de/node?id=1106907 https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20120712-1106907-1-6 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025374042&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT schneidersebastianeckehart solvationofproteinbindingsitesandoptimisationofproteinproteincomplexprediction

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