Computer simulations of protein structures and interactions:
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | German |
| Veröffentlicht: |
Berlin u.a.
Springer
1995
|
| Schriftenreihe: | Lecture notes in chemistry
66 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XII, 282 S. graph. Darst. |
| ISBN: | 3540601333 0387601333 |
Internformat
MARC
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| 100 | 1 | |a Fraga, Serafin |d 1931- |e Verfasser |0 (DE-588)120518120 |4 aut | |
| 245 | 1 | 0 | |a Computer simulations of protein structures and interactions |c S. Fraga ; J. M. R. Parker ; J. M. Pocock |
| 264 | 1 | |a Berlin u.a. |b Springer |c 1995 | |
| 300 | |a XII, 282 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Lecture notes in chemistry |v 66 | |
| 650 | 7 | |a Computersimulaties |2 gtt | |
| 650 | 7 | |a Eiwitten |2 gtt | |
| 650 | 7 | |a Kwantummechanica |2 gtt | |
| 650 | 7 | |a Molecular design |2 gtt | |
| 650 | 7 | |a Molecular modelling |2 gtt | |
| 650 | 4 | |a Protéines - Structure - Simulation par ordinateur | |
| 650 | 7 | |a Protéines - Structure - Simulation par ordinateur |2 ram | |
| 650 | 7 | |a Structuur |2 gtt | |
| 650 | 4 | |a Technologie des protéines | |
| 650 | 7 | |a Technologie des protéines |2 ram | |
| 650 | 4 | |a Protein engineering | |
| 650 | 4 | |a Proteins |x Structure |x Computer simulation | |
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| 700 | 1 | |a Parker, J. M. Robert |e Verfasser |4 aut | |
| 700 | 1 | |a Pocock, Jennifer M. |e Verfasser |4 aut | |
| 830 | 0 | |a Lecture notes in chemistry |v 66 |w (DE-604)BV000000216 |9 66 | |
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Datensatz im Suchindex
| _version_ | 1807323874694529024 |
|---|---|
| adam_text |
TABLE
OF
CONTENTS
1
INTRODUCTION
.
1
PROTEIN
FOLDING
.
3
2
AMINO
ADDS,
PEPTIDES,
AND
PROTEINS
.
4
2.1
INTRODUCTION
.
4
2.2
AMINO
ACIDS
.
9
2.3
PEPTIDE
AND
PROTEIN
CHAINS
.
13
2.3.1
PRIMARY
STRUCTURE
.
13
2.3.2
SECONDARY
STRUCTURE
.
16
2.3.3
TERTIARY
STRUCTURE
.
18
2.3.4
QUATERNARY
STRUCTURE
.
24
2.4
POST-TRANSLATION
MODIFICATIONS
.
24
THEORETICAL
FORMULATION
.
26
3
QUANTUM
MECHANICS
.
27
3.1
THE
SCHRODINGER
EQUATION
.
27
3.1.1
THE
HAMILTONIAN
OPERATOR
.
28
3.1.2.
EIGENFUNCTIONS
AND
EIGENVALUES
.
29
3.2.
ORBITALS
AND
SPIN-ORBITALS
.
.
.
30
3.3
PERTURBATION
THEORY
FOR
NON-DEGENERATE
STATES
.
33
3.3.1.
ZERO
AND
FIRST-ORDER
APPROXIMATIONS
.
34
3.4
VARIATIONAL
METHOD
.
37
3.4.1.
THE
VARIATIONAL
PRINCIPLE
.
37
3.4.2.
SELF-CONSISTENT
FIELD
THEORY
.
38
3.5
THE
EXPANSION
APPROXIMATION
.
42
3.5.1
MATRIX
REPRESENTATION
OF
THE
HARTREE-FOCK
EQUATIONS
.
42
3.5.2
EIGENVECTORS
AND
ORBITAL
ENERGIES
.
45
3.5.3
PRACTICAL
DETAILS
.
46
3.6
BEYOND
HARTREE-FOCK
.
47
3.7
ANALYSIS
OF
THE
RESULTS
.
49
3.7.1
POPULATION
ANALYSIS
.
50
3.7.2
EFFECTIVE
CHARGES
AND
ATOM
CLASSES
.
52
VIII
3.8
MOLECULAR
INTERACTIONS
AND
ASSOCIATIONS
.
55
3.8.1
BINDING
ENERGY
.
56
3.9
SUMMARY
.
57
4
STATISTICAL
MECHANICS
.
58
4.1
BASIC
CONCEPTS
.
58
4.2
THE
CANONICAL
ENSEMBLE
.
59
4.2.1
THE
PARTITION
FUNCTION
.
60
4.2.2
THERMODYNAMIC
PROPERTIES
.
62
4.2.3
THE
MOLECULAR
PARTITION
FUNCTION
.
63
4.3
NUMERICAL
CALCULATIONS
.
66
4.3.1
THE
MONTE
CARLO
METHOD
.
67
4.4
SUMMARY
.
70
5
MOLECULAR
MECHANICS:
THE
POTENTIAL
ENERGY
FUNCTION
.
71
5.1
FORCES
IN
PROTEIN
FOLDING
.
72
5.2
THEORETICAL
FORMULATION
OF
MOLECULAR
INTERACTIONS
.
73
5.2.1
CHARGES,
MOMENTS,
AND
FIELDS
.
73
5.2.2
THE
MULTIPOLE
EXPANSION
.
79
5.2.3
LONG-RANGE
ELECTROSTATIC
INTERACTION
BETWEEN
RIGID
MOLECULES
.
80
5.2.4
THE
ATOM-PAIR
POTENTIAL
APPROXIMATION
.
85
5.2.5
SHORT-RANGE
ELECTROSTATIC
INTERACTION
BETWEEN
RIGID
MOLECULES
.
86
5.3
DETERMINATION
OF
A
THEORETICAL
POTENTIAL
ENERGY
FUNCTION
.
87
5.3.1
THE
METHOD
OF
CLEMENTI
.
87
5.3.2
TRANSFORMATION
OF
THE
EXPANSION
PARAMETERS
.
90
5.3.3
ADDITIONAL
TERMS
FOR
NON-RIGID
MOLECULES
.
93
5.3.4
OTHER
INTERACTIONS
.
95
5.3.5
THE
USE
OF
A
DIELECTRIC
CONSTANT
.
96
5.4
SUMMARY
.
96
6
MOLECULAR
MECHANICS:
COMPUTER
SIMULATIONS
.
98
6.1
GENERAL
CONSIDERATIONS
.
98
6.2
ENERGY
MINIMIZATION
.
99
6.2.1
MODELING
OF
ISOLATED
PEPTIDE
STRUCTURES
.
100
6.2.2
MOLECULAR
ASSOCIATIONS
.
110
63
MONTE
CARLO
SIMULATIONS
.
113
6.3.1
THE
BASIC
APPROACH
.
113
6.3.2
MONTE
CARLO
MINIMIZATION
WITH/WITHOUT
THERMALIZATION/ANNEALING
.
114
6.4
MOLECULAR
DYNAMICS
.
115
6.4.1
THE
EQUATIONS
OF
MOTION
.
116
6.4.2
SOLUTIONS
OF
THE
EQUATIONS
OF
MOTION
.
118
6.4.3
PRACTICAL
DETAILS
.
120
6.4.4
ANALYSIS
OF
THE
RESULTS
.
123
IX
6.5
MONTE
CARLO/MOLECULAR
DYNAMICS
SIMULATIONS
.
126
7
PRACTICAL
OVERVIEW
.
128
EXPERIMENTAL
AND
THEORETICAL
DATA
.
130
8
DATABASES
.
131
8.1
STRUCTURAL
DATA
.
131
8.1.1
BROOKHAVEN
PROTEIN
DATA
BANK
AND
CAMBRIDGE
STRUCTURAL
DATABASE
.
131
8.1.2
ADDITIONAL
DATABASES
.
132
8.2
PHYSICO-CHEMICAL
DATA
.
134
8.2.1
HYDROPHILICITY,
FLEXIBILITY,
ACCESSIBILITY,
AND
RECOGNITION
PARAMETERS
FOR
INDIVIDUAL
AMINO
ACIDS
.
134
8.2.2
PROFILES
.
137
8.3
SUMMARY
.
138
MODELING
OF
ISOLATED
SYSTEMS
AND
ASSOCIATIONS.
139
9
PREDICTION
OF
SECONDARY
STRUCTURES
.
140
9.1
INTRODUCTION
.
140
9.2
NON-LEARNING
ALGORITHMS
.
142
9.2.1
PTITSYN-FINKELSTEIN
.
142
9.2.2
CHOU-FASMAN
.
143
9.2.3
GAMIER-OSGUTHORPE-ROBSON
(GOR)
.
145
9.2.4
UM
.
145
9.2.5
COHEN
ABARBANEL-KUNTZ-FLETTERICK
(CAKF)
.
146
9.2.6
LAMBERT-SCHERAGA
.
150
9.2.7
COMBINATION
METHODS
.
150
9.3
LEARNING
SYSTEMS
.
151
9.3.1
NON-SYMBOLIC
NETWORKS
.
153
9.3.2
SYMBOLIC
NETWORKS
.
157
9.4
SUMMARY
.
162
10
MODELING
OF
TERTIARY
STRUCTURES
.
164
10.1
INTRODUCTION
.
164
10.2
THE
PROBLEM
OF
MULTIPLE
MINIMA
.
165
10.3
ENERGY
MINIMIZATION
.
168
10.3.1
REFINEMENT
OF
CRYSTALLOGRAPHIC
STRUCTURES
.
169
10.3.2
LOW-RESOLUTION
PREDICTIONS
.
170
10.3.3
BUILD-UP
PROCEDURES
.
171
(A)
RESIDUE-BY-RESIDUE
.
171
(B)
STEP-BY-STEP
.
175
(C)
FROM
STRUCTURAL
UNITS
AND
FLEXIBLE
JOINTS
.
175
(D)
HOMOLOGY/COMPARATIVE
MODELING
.
177
X
10.3.4
THE
GENETIC
ALGORITHM
.
181
10.4
MOLECULAR
DYNAMICS
SIMULATIONS
.
182
10.4.1
ILLUSTRATIVE
APPLICATIONS
.
183
10.4.2
PRACTICAL
DIFFICULTIES
.
185
I
10.4.3
THE
SOLVENT
EFFECT
.
188
10.5
LONG-TIME
DYNAMICS
.
189
10.6
SIMULATED
ANNEALING
.
191
10.7
HYBRID
DYNAMICS/MONTE
CARLO
SIMULATIONS
.
194
11
MOLECULAR
ASSOCIATIONS
.
196
11.1
INTRODUCTION
.
196
112
FAST
EVALUATION
OF
INTERACTION
ENERGIES
.
197
11.3
SOLVATION
.
199
11.3.1
POTENTIAL
ENERGY
FUNCTIONS
.
200
11.3.2
MOLECULAR
DYNAMICS
SIMULATIONS
.
203
11.3.3
OTHER
APPROACHES
.
204
11.4
MOLECULAR
RECOGNITION
.
205
11.4.1
MOLECULAR
SURFACES
AND
BINDING
SITES
.
206
11.4.2
DOCKING
PROCEDURES
.
208
APPLICATIONS
.
214
12
STRUCTURE-AIDED
MOLECULAR
DESIGN
.
.
215
12.1
INTRODUCTION
.
215
122
DE
NOVO
PEPTIDE
AND
PROTEIN
DESIGN
.
216
12.2.1
CONDUCTIVE
POLYMERS
.
216
12.2.2
MOLECULAR
SWITCHES
.
217
12.2.3
SYNTHETIC
VACCINES
.
218
12.2.4
PEPZYMES
.
224
12.3
DRUG
DESIGN
.
225
12.3.1
GENERAL
CONSIDERATIONS
.
225
12.3.2
LIBRARIES
.
226
12.3.3
SITE-DIRECTED
LIGANDS
.
228
12.3.4
STRUCTURE-ACTIVITY
RELATIONSHIPS
.
229
12.3.5
PEPTIDOMIMETICS
.
231
BIBLIOGRAPHY
.
.
.
235
REFERENCES
.
235
REFERENCE
TEXTS
.
265
APPENDIX
1.
CONSTANTS
AND
UNITS
.
268
AL.L
CONSTANTS
.
268
A1.2
UNITS
.
268
APPENDIX
2.
AMINO
ADD
DATA
.
.
.
269 |
| any_adam_object | 1 |
| author | Fraga, Serafin 1931- Parker, J. M. Robert Pocock, Jennifer M. |
| author_GND | (DE-588)120518120 |
| author_facet | Fraga, Serafin 1931- Parker, J. M. Robert Pocock, Jennifer M. |
| author_role | aut aut aut |
| author_sort | Fraga, Serafin 1931- |
| author_variant | s f sf j m r p jmr jmrp j m p jm jmp |
| building | Verbundindex |
| bvnumber | BV010293515 |
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| callnumber-label | QP551 |
| callnumber-raw | QP551 |
| callnumber-search | QP551 |
| callnumber-sort | QP 3551 |
| callnumber-subject | QP - Physiology |
| classification_rvk | VC 6300 WC 3420 WD 5100 |
| classification_tum | PHY 821f CHE 820f CHE 806f CHE 026f |
| ctrlnum | (OCoLC)845032825 (DE-599)BVBBV010293515 |
| dewey-full | 574.19/245 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 574 - [Unassigned] |
| dewey-raw | 574.19/245 |
| dewey-search | 574.19/245 |
| dewey-sort | 3574.19 3245 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Physik Biologie Chemie |
| format | Book |
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| id | DE-604.BV010293515 |
| illustrated | Illustrated |
| indexdate | 2024-08-14T01:19:20Z |
| institution | BVB |
| isbn | 3540601333 0387601333 |
| language | German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-006848266 |
| oclc_num | 845032825 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-29T DE-703 DE-91G DE-BY-TUM DE-83 DE-11 |
| owner_facet | DE-355 DE-BY-UBR DE-29T DE-703 DE-91G DE-BY-TUM DE-83 DE-11 |
| physical | XII, 282 S. graph. Darst. |
| publishDate | 1995 |
| publishDateSearch | 1995 |
| publishDateSort | 1995 |
| publisher | Springer |
| record_format | marc |
| series | Lecture notes in chemistry |
| series2 | Lecture notes in chemistry |
| spelling | Fraga, Serafin 1931- Verfasser (DE-588)120518120 aut Computer simulations of protein structures and interactions S. Fraga ; J. M. R. Parker ; J. M. Pocock Berlin u.a. Springer 1995 XII, 282 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Lecture notes in chemistry 66 Computersimulaties gtt Eiwitten gtt Kwantummechanica gtt Molecular design gtt Molecular modelling gtt Protéines - Structure - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur ram Structuur gtt Technologie des protéines Technologie des protéines ram Protein engineering Proteins Structure Computer simulation Proteine (DE-588)4076388-2 gnd rswk-swf Struktur (DE-588)4058125-1 gnd rswk-swf Wechselwirkung (DE-588)4064937-4 gnd rswk-swf Computersimulation (DE-588)4148259-1 gnd rswk-swf Molekulardynamik (DE-588)4170370-4 gnd rswk-swf Proteine (DE-588)4076388-2 s Struktur (DE-588)4058125-1 s Computersimulation (DE-588)4148259-1 s DE-604 Wechselwirkung (DE-588)4064937-4 s Molekulardynamik (DE-588)4170370-4 s Parker, J. M. Robert Verfasser aut Pocock, Jennifer M. Verfasser aut Lecture notes in chemistry 66 (DE-604)BV000000216 66 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006848266&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Fraga, Serafin 1931- Parker, J. M. Robert Pocock, Jennifer M. Computer simulations of protein structures and interactions Lecture notes in chemistry Computersimulaties gtt Eiwitten gtt Kwantummechanica gtt Molecular design gtt Molecular modelling gtt Protéines - Structure - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur ram Structuur gtt Technologie des protéines Technologie des protéines ram Protein engineering Proteins Structure Computer simulation Proteine (DE-588)4076388-2 gnd Struktur (DE-588)4058125-1 gnd Wechselwirkung (DE-588)4064937-4 gnd Computersimulation (DE-588)4148259-1 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4058125-1 (DE-588)4064937-4 (DE-588)4148259-1 (DE-588)4170370-4 |
| title | Computer simulations of protein structures and interactions |
| title_auth | Computer simulations of protein structures and interactions |
| title_exact_search | Computer simulations of protein structures and interactions |
| title_full | Computer simulations of protein structures and interactions S. Fraga ; J. M. R. Parker ; J. M. Pocock |
| title_fullStr | Computer simulations of protein structures and interactions S. Fraga ; J. M. R. Parker ; J. M. Pocock |
| title_full_unstemmed | Computer simulations of protein structures and interactions S. Fraga ; J. M. R. Parker ; J. M. Pocock |
| title_short | Computer simulations of protein structures and interactions |
| title_sort | computer simulations of protein structures and interactions |
| topic | Computersimulaties gtt Eiwitten gtt Kwantummechanica gtt Molecular design gtt Molecular modelling gtt Protéines - Structure - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur ram Structuur gtt Technologie des protéines Technologie des protéines ram Protein engineering Proteins Structure Computer simulation Proteine (DE-588)4076388-2 gnd Struktur (DE-588)4058125-1 gnd Wechselwirkung (DE-588)4064937-4 gnd Computersimulation (DE-588)4148259-1 gnd Molekulardynamik (DE-588)4170370-4 gnd |
| topic_facet | Computersimulaties Eiwitten Kwantummechanica Molecular design Molecular modelling Protéines - Structure - Simulation par ordinateur Structuur Technologie des protéines Protein engineering Proteins Structure Computer simulation Proteine Struktur Wechselwirkung Computersimulation Molekulardynamik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006848266&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000216 |
| work_keys_str_mv | AT fragaserafin computersimulationsofproteinstructuresandinteractions AT parkerjmrobert computersimulationsofproteinstructuresandinteractions AT pocockjenniferm computersimulationsofproteinstructuresandinteractions |