Numerical methods for the life scientist: binding and enzyme kinetics calculated with GNU Octave and MATLAB
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2011
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | IX, 149 S. graph. Darst. |
| ISBN: | 3642208193 9783642208195 |
Internformat
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| 245 | 1 | 0 | |a Numerical methods for the life scientist |b binding and enzyme kinetics calculated with GNU Octave and MATLAB |c Heino Prinz |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2011 | |
| 300 | |a IX, 149 S. |b graph. Darst. | ||
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Datensatz im Suchindex
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|---|---|
| adam_text |
IMAGE 1
CONTENTS
1 INTRODUCTION 1
REFERENCES 4
2 THEBASICS 5
2.1 EQUATIONS FOR FIRST AND SECOND ORDER REACTIONS 5
2.2 EQUILIBRIUM BINDING TO TWO SITES 7
2.3 EQUILIBRIUM BINDING TO ANY NUMBER OF SITES 9
2.4 WRITING DIFFERENTIAL EQUATIONS FOR TWO SITE BINDING 10 2.5 WRITING
DIFFERENTIAL EQUATIONS FOR ANY REACTION SCHEME 12 2.6 ANALYTICAL AND
NUMERICAL SOLUTIONS 12
3 CLASSICAL ANALYTICAL SOLUTIONS 15
3.1 ANALYTICAL SOLUTIONS FOR EQUILIBRIUM BINDING 15
3.1.1 DIRECT BINDING CURVES 15
3.1.2 DOUBLE RECIPROCAL PLOTS 17
3.1.3 COMPARISON OF SCATCHARD PLOTS AND DOUBLE RECIPROCAL PLOTS 18
3.1.4 LINEWEAVER-BURK PLOTS 21
3.1.5 DOSE-RESPONSE CURVES AND HILL COEFFICIENTS 23
3.2 ANALYTICAL SOLUTIONS FOR BINDING KINETICS 24
3.2.1 EXPONENTIAL DECAY 25
3.2.2 HALF-LOGARITHMIC PLOTS 26
3.2.3 INITIAL VELOCITY OF ASSOCIATION KINETICS 27
3.2.4 PSEUDO FIRST-ORDER KINETICS 28
3.2.5 MULTIPLE EXPONENTIAL FITS 28
REFERENCES 29
4 GETTING STARTED WITH OCTAVE 31
4.1 INSTALLATION INSTRUCTIONS 31
4.2 TYPING THE FIRST COMMANDS 32
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/1010803921
DIGITALISIERT DURCH
IMAGE 2
VIII CONTENTS
4.3 WRITING A PROGRAM 34
4.4 SETTING UP A WORK ENVIRONMENT FOR OCTAVE: ARRANGEMENT OF EDITOR,
TERMINAL, AND PLOT WINDOW 36
4.5 THE MATLAB ENVIRONMENT 37
4.6 ARRAYS, VECTORS, AND MATRICES 38
4.7 A VERY ELEMENTARY TUTORIAL FOR GNU OCTAVE AND MATLAB 39 4.8
RECOMMENDED LITERATURE FOR OCTAVE/MATLAB 40
REFERENCES 40
5 EQUILIBRIUM BINDING 43
5.1 SOLVING NONLINEAR EQUATIONS FOR EQUILIBRIUM BINDING 43 5.2
EQUILIBRIUM BINDING TO ONE SITE (EQL.M) 44
5.3 EQUILIBRIUM BINDING TO TWO SITES (EQ2.M) 50
5.4 EQUILIBRIUM BINDING TO TWO SITES IN THE PRESENCE OF INHIBITOR (EQ3.
M) 52
5.5 ALLOSTERIC INTERACTIONS OF SUBUNITS (EQ4 . M) 57
5.6 ALLOSTERIC ACTIVATORS AND INHIBITORS (EQ5. M) 62
5.7 DOSE-RESPONSE CURVES (EQ6 .M) 64
5.8 MULTIPLE ALLOSTERIC INHIBITION (EQ 7. M) 67
REFERENCES 70
6 BINDING KINETICS 71
6.1 SOLVING DIFFERENTIAL EQUATIONS IN GNU OCTAVE AND MATLAB 71 6.2
KINETICS OF LIGAND BINDING TO ONE SITE ( K I N L. M) 73
6.3 BINDING TO ONE SITE FOLLOWED BY A CONFORMATIONAL CHANGE OF THE
RECEPTOR (KIN2 . M) 77
6.4 DISSOCIATION KINETICS: CHASE WITH INHIBITOR (KIN3 . M) 81 6.5
FACILITATED DISSOCIATION (KIN4 .M) 84
6.6 SEQUENTIAL BINDING AND OBSTRUCTED DISSOCIATION (KIN5.M) 87 6.7
IRREVERSIBLE INHIBITION (KIN 6 .M) 91
REFERENCES 95
7 ENZYME KINETICS 97
7.1 PROGRESS CURVES ( E N ZL .M) 97
7.2 PROGRESS CURVES FOR A WEAK SUBSTRATE (ENZLB.M) 99
7.3 MICHAELIS-MENTEN ENZYME KINETICS (ENZ2 .M) 101
7.4 LINEWEAVER-BURKPLOTS FROM PROGRESS CURVES (ENZ3.M) 102 7.5 SUBSTRATE
INHIBITION (ENZ 4. M) 107
7.6 ENZYME INHIBITION WITH REVERSIBLE INHIBITORS (ENZ5.M) I LL
REFERENCES 118
8 FITTING THE DATA 119
8.1 MULTI-PARAMETER FITS AND CORRELATION OF PARAMETERS (FIT 1 .M) 119
8.1.1 THE SAMPLE PROGRAM FIT 1. M 120
IMAGE 3
CONTENTS IX
8.1.2 STRATEGIES TO FIT CORRELATED PARAMETERS 123
8.2 EXPERIMENTAL SETUP 124
8.3 ENTERING THE EXPERIMENTAL DATA (FIT2 . M) 125
8.4 FITTING SUBSTRATE INHIBITION 127
8.4.1 GENERATING SAMPLE DATA (FIT 3. M) 128
8.4.2 CALCULATING STEADY STATE EQUILIBRIA (FIT 4. M) 129
8.4.3 GLOBAL FIT OFPROGRESS CURVES (FIT5.M) 136
REFERENCES 141
9 APPENDIX: INSTALLING GNU OCTAVE FOR MAC OS AND LINUX 143 9.1
INSTALLATION INSTRUCTIONS FOR MAC OS X 143
9.2 INSTALLATION INSTRUCTIONS FOR LINUX 144
INDEX 147 |
| any_adam_object | 1 |
| author | Prinz, Heino |
| author_facet | Prinz, Heino |
| author_role | aut |
| author_sort | Prinz, Heino |
| author_variant | h p hp |
| building | Verbundindex |
| bvnumber | BV039600279 |
| classification_rvk | WC 7000 |
| ctrlnum | (OCoLC)725062759 (DE-599)DNB1010803921 |
| dewey-full | 572.4401518 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.4401518 |
| dewey-search | 572.4401518 |
| dewey-sort | 3572.4401518 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
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| id | DE-604.BV039600279 |
| illustrated | Illustrated |
| indexdate | 2024-07-21T00:11:01Z |
| institution | BVB |
| isbn | 3642208193 9783642208195 |
| language | English |
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| physical | IX, 149 S. graph. Darst. |
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| publisher | Springer |
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| spelling | Prinz, Heino Verfasser aut Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB Heino Prinz Berlin [u.a.] Springer 2011 IX, 149 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Reaktionskinetik (DE-588)4048655-2 gnd rswk-swf Programm (DE-588)4047394-6 gnd rswk-swf Biowissenschaften (DE-588)4129772-6 gnd rswk-swf Chemisches Gleichgewicht (DE-588)4147642-6 gnd rswk-swf Numerisches Verfahren (DE-588)4128130-5 gnd rswk-swf Ligand Biochemie (DE-588)4606532-5 gnd rswk-swf Enzymkinetik (DE-588)4133166-7 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Ligand Biochemie (DE-588)4606532-5 s Reaktionskinetik (DE-588)4048655-2 s Chemisches Gleichgewicht (DE-588)4147642-6 s Enzymkinetik (DE-588)4133166-7 s Numerisches Verfahren (DE-588)4128130-5 s Programm (DE-588)4047394-6 s DE-604 Biowissenschaften (DE-588)4129772-6 s Bioinformatik (DE-588)4611085-9 s 1\p DE-604 Erscheint auch als Online-Ausgabe 978-3-642-20820-1 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3708389&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024451178&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Prinz, Heino Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB Reaktionskinetik (DE-588)4048655-2 gnd Programm (DE-588)4047394-6 gnd Biowissenschaften (DE-588)4129772-6 gnd Chemisches Gleichgewicht (DE-588)4147642-6 gnd Numerisches Verfahren (DE-588)4128130-5 gnd Ligand Biochemie (DE-588)4606532-5 gnd Enzymkinetik (DE-588)4133166-7 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4048655-2 (DE-588)4047394-6 (DE-588)4129772-6 (DE-588)4147642-6 (DE-588)4128130-5 (DE-588)4606532-5 (DE-588)4133166-7 (DE-588)4611085-9 |
| title | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB |
| title_auth | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB |
| title_exact_search | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB |
| title_full | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB Heino Prinz |
| title_fullStr | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB Heino Prinz |
| title_full_unstemmed | Numerical methods for the life scientist binding and enzyme kinetics calculated with GNU Octave and MATLAB Heino Prinz |
| title_short | Numerical methods for the life scientist |
| title_sort | numerical methods for the life scientist binding and enzyme kinetics calculated with gnu octave and matlab |
| title_sub | binding and enzyme kinetics calculated with GNU Octave and MATLAB |
| topic | Reaktionskinetik (DE-588)4048655-2 gnd Programm (DE-588)4047394-6 gnd Biowissenschaften (DE-588)4129772-6 gnd Chemisches Gleichgewicht (DE-588)4147642-6 gnd Numerisches Verfahren (DE-588)4128130-5 gnd Ligand Biochemie (DE-588)4606532-5 gnd Enzymkinetik (DE-588)4133166-7 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Reaktionskinetik Programm Biowissenschaften Chemisches Gleichgewicht Numerisches Verfahren Ligand Biochemie Enzymkinetik Bioinformatik |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=3708389&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024451178&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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