Molecular modeling: basic principles and applications
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Weinheim [u.a.]
VCH
1996
|
| Series: | Methods and principles in medicinal chemistry
5 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | 2. Aufl. u.d.T.: Molecular modeling |
| Physical Description: | XII, 194 S. Ill., graph. Darst. |
| ISBN: | 3527293841 |
Staff View
MARC
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| 100 | 1 | |a Höltje, Hans-Dieter |e Verfasser |0 (DE-588)135841305 |4 aut | |
| 245 | 1 | 0 | |a Molecular modeling |b basic principles and applications |c by Hans-Dieter Höltje and Gerd Folkers |
| 264 | 1 | |a Weinheim [u.a.] |b VCH |c 1996 | |
| 300 | |a XII, 194 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods and principles in medicinal chemistry |v 5 | |
| 500 | |a 2. Aufl. u.d.T.: Molecular modeling | ||
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| 830 | 0 | |a Methods and principles in medicinal chemistry |v 5 |w (DE-604)BV035418617 |9 5 | |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007347922&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
Record in the Search Index
| _version_ | 1805071220859731968 |
|---|---|
| adam_text |
CONTENTS
PREFACE
V
A
PERSONAL
FOREWORD
.
VII
1
INTRODUCTION
.
1
1.1
MODERN
HISTORY
OF
MOLECULAR
MODELING
.
2
1.2
DO
TODAY
'
S
MOLECULAR
MODELING
METHODS
ILLUSTRATE
ONLY
THE
LUKRETIAN
WORLD?
.
3
1.3
WHAT
ARE
MODELS
USED
FOR?
.
4
1.4
MOLECULAR
MODELING USES ALL
FOUR
TYPES
FOR
MODEL
BUILDING
.
4
1.5
THE
FINAL
STEP
IS
DESIGN
.
4
1.6
THE
SCOPE
OF
THE
BOOK
.
5
2
SMALL
MOLECULES
.
9
2.1
GENERATION
OF
3D
COORDINATES
.
9
2.1.1
CRYSTAL
DATA
.
9
2.1.2
FRAGMENT
LIBRARIES
.
10
2.1.3
SKETCH
APPROACH
.
12
2.2
COMPUTATIONAL
TOOLS
FOR
GEOMETRY
OPTIMIZATION
.
13
2.2.1
FORCE
FIELDS
.
13
2.2.2
GEOMETRY
OPTIMIZATION
.
15
2.2.3
ENERGY-MINIMIZING
PROCEDURES
.
16
2.2.3.1
STEEPEST
DESCENT
MINIMIZER
.
17
2.2.3.2
CONJUGATE
GRADIENT
METHOD
.
17
2.2.3.3
NEWTON-RAPHSON
MINIMIZER
.
17
2.2.4
USE
OF
CHARGES,
SOLVATION
EFFECTS
.
18
2.2.5
QUANTUM
MECHANICAL
METHODS
.
19
2.2.5.1
AB
INITIO
METHODS
.
19
2.2.5.2
SEMIEMPIRICAL
MOLECULAR
ORBITAL
METHODS
.
21
2.3
CONFORMATIONAL
ANALYSIS
.
23
2.3.1
CONFORMATIONAL
ANALYSIS
USING
SYSTEMATIC
SEARCH
PROCEDURES
.
25
2.3.2
CONFORMATIONAL
ANALYSIS
USING
MONTE
CARLO
METHODS
.
29
2.3.3
CONFORMATIONAL
ANALYSIS
USING
MOLECULAR
DYNAMICS
.
29
X
CONTENTS
2.4
DETERMINATION
OF
MOLECULAR
INTERACTION
POTENTIALS
.
37
2.4.1
MOLECULAR
ELECTROSTATIC
POTENTIALS
(MEPS)
.
37
2.4.1.1
METHODS
FOR
CALCULATING
ATOMIC
POINT
CHARGES
.
38
2.4.1.2
METHODS
FOR
GENERATING
MEPS
.
42
2.4.2
MOLECULAR
INTERACTION
FIELDS
.
43
2.4.2.1
CALCULATION
OF
GRID
FIELDS
.
45
2.4.2.2
HOW
GRID
FIELDS
CAN
BE
EXPLOITED
.
47
2.4.2.3
USE
OF
CHEMOMETRICS:
THE
COMFA
METHOD
.
49
2.4.3
HYDROPHOBIC
INTERACTIONS
.
49
2.4.3.1
LOG
P
AS
A
MEASURE
OF
LIPOPHILICITY
.
50
2.4.3.2
THE
HYDROPATHIC
FIELD
.
50
2.4.3.3
DISPLAY
OF
PROPERTIES
ON
A
MOLECULAR
SURFACE
.
51
2.5
PHARMACOPHORE
IDENTIFICATION
.
55
2.5.1
MOLECULES
TO
BE
MATCHED
.
55
2.5.2
ATOM-BY-ATOM
SUPERPOSITION
.
56
2.5.3
SUPERPOSITION
OF
MOLECULAR
FIELDS
.
58
2.6
THE
USE
OF
DATA
BANTS
.
60
2.6.1
CONVERSION
OF
2D
STRUCTURAL
DATA
INTO
3D
FORM
.
60
2.6.2
3D
SEARCHING
.
61
3
EXAMPLE
FOR
SMALL
MOLECULE
MODELING:
SEROTONIN
RECEPTOR
LIGANDS
.
65
3.1
DEFINITION
OF
THE
SEROTONINERGIC
PHARMACOPHORE
.
65
3.2
THE
MOLECULAR
INTERACTION
FIELD
.
69
3.3
CONSTRUCTION
OF
A
5-HT
2A
RECEPTOR
BINDING
SITE
MODEL
.
71
3.4
CALCULATION
OF
INTERACTION
ENERGIES
.
73
3.5
VALIDATION
OF
THE
MODEL
.
74
4
INTRODUCTION
TO
PROTEIN
MODELING
.
77
4.1
WHERE
AND
HOW
TO
GET
INFORMATION
ON
PROTEINS
.
77
4.2
TERMINOLOGY
AND
PRINCIPLES
OF
PROTEIN
STRUCTURE
.
81
4.2.1
CONFORMATIONAL
PROPERTIES
OF
PROTEINS
.
81
4.2.2
TYPES
OF
SECONDARY
STRUCTURAL
ELEMENTS
.
84
4.2.2.1
THEA-HELIX
.
84
4.2.2.2
THE/3-SHEET
.
85
4.2.2.3
TURNS
.
87
4.2.3
HOMOLOGOUS
PROTEINS
.
88
4.3
KNOWLEDGE-BASED
PROTEIN
MODELING
.
91
4.3.1
PROCEDURES
FOR
SEQUENCE
ALIGNMENTS
.
92
4.3.2
DETERMINATION
AND
GENERATION
OF
STRUCTURALLY
CONSERVED
REGIONS
(SCRS)
.
96
4.3.3
CONSTRUCTION
OF
STRUCTURALLY
VARIABLE
REGIONS
(SVRS)
.
98
4.3.4
SIDE
CHAIN
MODELING
.
99
CONTENTS
XI
4.3.5
DISTANCE
GEOMETRY
APPROACH
.
101
4.3.6
SECONDARY
STRUCTURE
PREDICTION
.
101
4.3.7
ENERGY-BASED
MODELING
METHODS
.
103
4.4
OPTIMIZATION
PROCEDURES
-
MODEL
REFINEMENT
-
MOLECULAR
DYNAMICS
.
.
109
4.4.1
FORCE
FIELDS
FOR
PROTEIN
MODELING
.
109
4.4.2
GEOMETRY
OPTIMIZATION
.
110
4.4.3
THE
USE
OF
MOLECULAR
DYNAMICS
SIMULATIONS
IN
MODEL
REFINEMENT
.
ILL
4.4.4
TREATMENT
OF
SOLVATED
SYSTEMS
.
113
4.4.5
LIGAND-BINDING
SITE
COMPLEXES
.
113
4.5
VALIDATION
OF
PROTEIN
MODELS
.
115
4.5.1
STEREOCHEMICAL
ACCURACY
.
116
4.5.2
PACKING
QUALITY
.
120
4.5.3
FOLDING
RELIABILITY
.
122
4.6
PROPERTIES
OF
PROTEINS
.
127
4.6.1
ELECTROSTACTIC
POTENTIAL
.
127
4.6.2
INTERACTION
POTENTIALS
.
130
4.6.3
HYDROPHOBICITY
.
130
5
EXAMPLE
FOR
THE
MODELING
OF
PROTEIN-LIGAND
COMPLEXES:
ANTIGEN
PRESENTATION
BY
MHC
CLASS
I
.
133
5.1
BIOCHEMICAL
AND
PHARMACOLOGICAL
DESCRIPTION
OF
THE
PROBLEM
.
133
5.1.1
ANTIGENIC
PROTEINS
ARE
PRESENTED
AS
NONAPEPTIDES
.
134
5.1.2
PHARMACOLOGICAL
TARGET:
AUTOIMMUNE
REACTIONS
.
134
5.2
MOLECULAR
MODELING
OF
THE
ANTIGENIC
COMPLEX
BETWEEN
A
VIRAL
PEPTIDE
AND
A
CLASS
I
MHC
GLYCOPROTEIN
.
135
5.2.1
MODELING
OF
THE
LIGAND
.
135
5.2.2
HOMOLOGY MODELING
OF
THE
MHC
PROTEIN
.
136
5.2.2.1
PREPARATION
OF
THE
COORDINATES
.
137
5.2.2.2
BUILDING
THE
H-2L
D
MOLECULE
.
137
5.3
MOLECULAR
DYNAMICS
STUDIES
OF
MHC-PEPTIDE
COMPLEXES
.
146
5.3.1
HLA-A2
-
THE
FATE
OF
THE
COMPLEX
DURING
MOLECULAR
DYNAMICS
SIMULATIONS
.
146
5.3.2
HLS-B*2705
.
148
5.3.2.1
THE
FATE
OF
THE
COMPLEX
DURING
MOLECULAR
DYNAMICS
SIMULATIONS
.
150
5.4
ANALYSIS
OF
MODELS
THAT
EMERGED
FROM
MOLECULAR
DYNAMICS
SIMULATIONS
.
153
5.4.1
HYDROGEN
BONDING
NETWORK
.
153
5.4.2
ATOMIC
FLUCTUATIONS
.
154
5.4.3
SOLVENT-ACCESSIBLE
SURFACE
AREAS
.
157
5.4.4
INTERACTION
ENERGIES
.
158
5.5
SAR
OF
THE
ANTIGENIC
PEPTIDES
FROM
MOLECULAR
DYNAMICS
SIMULATIONS
AND
DESIGN
OF
NON-NATURAL
PEPTIDES
AS
HIGH-AFFINITY LIGANDS
FOR
A
MHC
I
PROTEIN
.
160
XII
CONTENTS
5.5.1
THE
DESIGN
OF
NEW
LIGANDS
.
160
5.5.2
EXPERIMENTAL
VALIDATION
OF
THE
DESIGNED
LIGAND
.
163
5.6
SUMMARY
AND
CONCLUSION
.
164
APPENDICES
.
165
INDEX
.
177 |
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| author | Höltje, Hans-Dieter Folkers, Gerd 1953- |
| author_GND | (DE-588)135841305 (DE-588)120208857 |
| author_facet | Höltje, Hans-Dieter Folkers, Gerd 1953- |
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| id | DE-604.BV010979674 |
| illustrated | Illustrated |
| indexdate | 2024-07-20T04:34:22Z |
| institution | BVB |
| isbn | 3527293841 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-007347922 |
| oclc_num | 633113427 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-703 DE-91G DE-BY-TUM DE-20 DE-634 |
| owner_facet | DE-355 DE-BY-UBR DE-703 DE-91G DE-BY-TUM DE-20 DE-634 |
| physical | XII, 194 S. Ill., graph. Darst. |
| publishDate | 1996 |
| publishDateSearch | 1996 |
| publishDateSort | 1996 |
| publisher | VCH |
| record_format | marc |
| series | Methods and principles in medicinal chemistry |
| series2 | Methods and principles in medicinal chemistry |
| spelling | Höltje, Hans-Dieter Verfasser (DE-588)135841305 aut Molecular modeling basic principles and applications by Hans-Dieter Höltje and Gerd Folkers Weinheim [u.a.] VCH 1996 XII, 194 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods and principles in medicinal chemistry 5 2. Aufl. u.d.T.: Molecular modeling Molekulardesign (DE-588)4265444-0 gnd rswk-swf Molekulardesign (DE-588)4265444-0 s DE-604 Folkers, Gerd 1953- Verfasser (DE-588)120208857 aut Methods and principles in medicinal chemistry 5 (DE-604)BV035418617 5 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007347922&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Höltje, Hans-Dieter Folkers, Gerd 1953- Molecular modeling basic principles and applications Methods and principles in medicinal chemistry Molekulardesign (DE-588)4265444-0 gnd |
| subject_GND | (DE-588)4265444-0 |
| title | Molecular modeling basic principles and applications |
| title_auth | Molecular modeling basic principles and applications |
| title_exact_search | Molecular modeling basic principles and applications |
| title_full | Molecular modeling basic principles and applications by Hans-Dieter Höltje and Gerd Folkers |
| title_fullStr | Molecular modeling basic principles and applications by Hans-Dieter Höltje and Gerd Folkers |
| title_full_unstemmed | Molecular modeling basic principles and applications by Hans-Dieter Höltje and Gerd Folkers |
| title_short | Molecular modeling |
| title_sort | molecular modeling basic principles and applications |
| title_sub | basic principles and applications |
| topic | Molekulardesign (DE-588)4265444-0 gnd |
| topic_facet | Molekulardesign |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007347922&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035418617 |
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