Open access databases and datasets for drug discovery:
Gespeichert in:
| Weitere Verfasser: | , , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Weinheim, Germany
Wiley-VCH
[2024]
|
| Schriftenreihe: | Methods and principles in medicinal chemistry
volume 83 |
| Schlagworte: | |
| Online-Zugang: | http://www.wiley-vch.de/publish/dt/books/ISBN978-3-527-34839-8/ Inhaltsverzeichnis |
| Beschreibung: | xxi, 323 Seiten Illustrationen, Diagramme 24.4 cm x 17 cm |
| ISBN: | 3527348395 9783527348398 |
Internformat
MARC
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| 245 | 1 | 0 | |a Open access databases and datasets for drug discovery |c edited by Antoine Daina, Michael Przewosny, and Vincent Zoete |
| 264 | 1 | |a Weinheim, Germany |b Wiley-VCH |c [2024] | |
| 300 | |a xxi, 323 Seiten |b Illustrationen, Diagramme |c 24.4 cm x 17 cm | ||
| 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 volume 83 | |
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| 653 | |a Biowissenschaften | ||
| 653 | |a CH61: Wirkstoffforschung u. -entwicklung | ||
| 653 | |a CHD0: Computational Chemistry u. Molecular Modeling | ||
| 653 | |a Chemie | ||
| 653 | |a Chemistry | ||
| 653 | |a Computational Chemistry & Molecular Modeling | ||
| 653 | |a Computational Chemistry u. Molecular Modeling | ||
| 653 | |a Drug Discovery & Development | ||
| 653 | |a LS38: Strukturbiologie | ||
| 653 | |a Life Sciences | ||
| 653 | |a Structural Biology | ||
| 653 | |a Strukturbiologie | ||
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Datensatz im Suchindex
| _version_ | 1808497153810628608 |
|---|---|
| adam_text |
CONTENTS
SERIES
EDITORS
PREFACE
XIII
RAIMUND
MANNHOLD
-
A
PERSONAL
OBITUARY
FROM
THE
SERIES
EDITORS
XVII
A
PERSONAL
FOREWORD
XXI
1
OPEN
ACCESS
DATABASES
AND
DATASETS
FOR
COMPUTER-AIDED
DRUG
DESIGN.
A
SHORT
LIST
USED
IN
THE
MOLECULAR
MODELLING
GROUP
OF
THE
SIB
1
ANTOINE
DAINA,
MARIA
JOSE
OJEDA-MONTES,
MAIIA
E.
BRAGINA,
ALESSANDRO
CUOZZO,
UTE
F.
ROHRIG,
MARTA
A.S.
PEREZ,
AND
VINCENT
ZOETE
REFERENCES
30
PART
I
SMALL
MOLECULES
39
2
PUBCHEM:
A
LARGE-SCALE
PUBLIC
CHEMICAL
DATABASE
FOR
DRUG
DISCOVERY
41
SUNGHWAN
KIM
AND
EVAN
E.
BOLTON
2.1
INTRODUCTION
41
2.2
DATA
CONTENT
AND
ORGANIZATION
42
2.3
TOOLS
AND
SERVICES
45
2.3.1
PUBCHEM
SEARCH
45
2.3.2
SUMMARY
PAGES
48
2.3.3
LITERATURE
KNOWLEDGE
PANEL
49
2.3.4
2D
AND
3D
NEIGHBORS
50
2.3.5
CLASSIFICATION
BROWSER
51
2.3.6
IDENTIFIER
EXCHANGE
SERVICE
52
2.3.7
PROGRAMMATIC
ACCESS
52
2.3.8
PUBCHEM
FTP
SITE
AND
PUBCHEMRDF
53
2.4
DRUG
AND
LEAD-LIKENESS
OF
PUBCHEM
COMPOUNDS
54
2.5
BIOACTIVITY
DATA
IN
PUBCHEM
56
2.6
COMPARISON
WITH
OTHER
DATABASES
57
2.7
USE
OF
PUBCHEM
DATA
FOR
DRUG
DISCOVERY
58
2.8
SUMMARY
59
ACKNOWLEDGMENTS
60
REFERENCES
60
VI
CONTENTS
3
DRUGBANK
ONLINE:
A
HOW-TO
GUIDE
67
CHRISTEN
M.
KLINGER,
JORDAN
COX,
DENISE
SO,
TEIRA
STAUTH,
MICHAEL
WILSON,
ALEX
WILSON,
AND
CRAIG
KNOX
3.1
3.2
3.2.1
3.2.2
3.2.2.1
3.2.2.2
3.2.2.3
3.2.2.4
3.2.2.5
3.2.2.6
3.2.2.7
3.3
3.3.1
3.3.1.1
3.3.1.2
3.3.1.3
3.3.2
3.3.2.1
3.3.2.2
3.3.3
3.4
3.5
INTRODUCTION
67
DRUGBANK
68
OVERVIEW
OF
DRUGBANK
68
DRUGBANK
DATASETS
69
DRUG
CARDS:
AN
OVERVIEW
AND
NAVIGATION
GUIDE
70
IDENTIFICATION
70
PHARMACOLOGY
71
CATEGORIES
73
PROPERTIES
73
TARGETS,
ENZYMES,
CARRIERS,
AND
TRANSPORTERS
73
REFERENCES
77
PROTOCOLS
77
GENERAL
WORKFLOWS
77
USING
DRUGBANK
ONLINE
'
S
SEARCH
FUNCTIONALITY
77
USING
DRUGBANK
ONLINE
'
S
ADVANCED
SEARCH
FUNCTIONALITY
80
BROWSING
DRUGS
USING
DRUGBANK
ONLINE
'
S
DRUG
CATEGORIES
83
IDENTIFYING
CHEMICALS
AND
RELEVANT
SEQUENCES
86
SEARCHING
USING
CHEMICAL
STRUCTURE
SEARCH
86
USING
SEQUENCE
SEARCH
TO
FIND
SIMILAR
TARGETS
89
EXTRACTING
DRUGBANK
DATASETS
FOR
ML
93
RESEARCH
USING
DRUGBANK
94
DISCUSSION
AND
CONCLUSIONS
95
REFERENCES
96
4
BIOISOSTERIC
REPLACEMENT
FOR
DRUG
DISCOVERY
SUPPORTED
BY
THE
SWISSBIOISOSTERE
DATABASE
101
ANTOINE
DAINA,
ALESSANDRO
CUOZZO,
MARTA
A.S.
PEREZ,
AND
VINCENT
ZOETE
4.1
4.1.1
4.1.2
INTRODUCTION
101
CONCEPT
OF
ISOSTERISM
AND
BIOISOSTERISM
101
CLASSICAL
VS.
NON-CLASSICAL
BIOISOSTERE
AND
FURTHER
MOLECULAR
REPLACEMENTS
102
4.1.3
4.2
4.2.1
4.2.2
4.2.3
4.2.4
4.2.5
4.3
4.3.1
4.3.2
4.3.3
BIOISOSTERIC
REPLACEMENT
IN
DRUG
DISCOVERY
105
CONSTRUCTION
AND
DISSEMINATION
OF
SWISSBIOISOSTERE
106
INTENTION
AND
REQUIREMENTS
106
BIOACTIVITY
DATA
107
NONSUPERVISED
MATCHED
MOLECULAR
PAIR
ANALYSIS
108
DATABASE
108
WEB
INTERFACE
109
CONTENT
OF
SWISSBIOISOSTERE
111
GLOBAL
CONTENT
111
BIOLOGICAL
AND
CHEMICAL
CONTEXTS
112
FRAGMENT
SHAPE
DIVERSITY
113
CONTENTS
VII
4.4
USAGE
OF
SWISSBIOISOSTERE
115
4.4.1
WEBSITE USAGE
115
4.4.2
MOST
FREQUENT
REQUESTS
117
4.4.3
EXAMPLES
RELATED
TO
DRUG
DISCOVERY
117
4.4.3.1
USE
CASES
117
4.4.3.2
REPLACING
UNWANTED
CHEMICAL
GROUPS
118
4.4.3.3
OPTIMIZATION
OF
PASSIVE
ABSORPTION
AND
BLOOD-BRAIN
BARRIER
DIFFUSION
122
4.4.3.4
REDUCTION
OF
FLEXIBILITY
124
4.4.3.5
REDUCTION
OF
AROMATICITY/ESCAPE
FROM
FLATLAND
128
4.5
CONCLUSIVE
REMARKS
133
ACKNOWLEDGMENT
133
REFERENCES
133
PART
II
MACROMOLECULAR
TARGETS
AND
DISEASES
139
5
THE
PROTEIN
DATA
BANK
(PDB)
AND
MACROMOLECULAR
STRUCTURE
DATA
SUPPORTING
COMPUTER-AIDED
DRUG
DESIGN
141
DAVID
ARMSTRONG,
JOHN
BERRISFORD,
PREETI
CHOUDHARY,
LUKAS
PRAVDA,
JAMES
TOLCHARD,
MIHOLY
VARADI,
AND
SAMEER
VELANKAR
5.1
INTRODUCTION
141
5.2
SMALL
MOLECULE
DATA
IN
PROTEIN
DATA
BANK
(PDB)
ENTRIES
142
5.2.1
WHAT
DATA
ARE
IN
THE
PDB
ARCHIVE?
142
5.2.2
DEFINITION
OF
SMALL
MOLECULES
IN
ONEDEP
145
5.3
SMALL
MOLECULE
DICTIONARIES
146
5.3.1
WWPDB
CHEMICAL
COMPONENT
DICTIONARY
(CCD)
146
5.3.2
THE
PEPTIDE
REFERENCE
DICTIONARY
147
5.4
ADDITIONAL
LIGAND
ANNOTATIONS
IN
THE
PDB
ARCHIVE
148
5.4.1
LINKAGE
INFORMATION
148
5.4.2
CARBOHYDRATES
149
5.5
VALIDATION
OF
LIGANDS
IN
THE
WORLDWIDE
PROTEIN
DATA
BANK
(WWPDB)
150
5.5.1
VARIOUS
CRITERIA
AND
SOFTWARE
USED
FOR
VALIDATING
LIGAND
IN
VALIDATION
REPORTS
150
5.5.2
IDENTIFICATION
OF
LIGAND
OF
INTEREST
(LOI)
151
5.5.3
GEOMETRIC
AND
CONFORMATIONAL
VALIDATION
152
5.5.4
LIGAND
FIT
TO
EXPERIMENTAL
ELECTRON
DENSITY
VALIDATION
152
5.5.5
ACCESSING
WWPDB
VALIDATION
REPORTS
FROM
PDBE
ENTRY
PAGES
154
5.5.6
OTHER
PLANNED
IMPROVEMENTS
TO
ENHANCE
LIGAND
VALIDATION
154
5.6
PDBE
TOOLS
FOR
LIGAND
ANALYSIS
155
5.6.1
LIGAND
INTERACTIONS
155
5.6.1.1
CLASSIFYING
LIGAND
INTERACTIONS
155
5.6.1.2
DATA
AVAILABILITY
156
5.6.2
LIGAND
ENVIRONMENT
COMPONENT
156
5.6.3
CHEMISTRY
PROCESS
AND
FTP
158
VIII
CONTENTS
5.6.4
5.7
5.7.1
5.7.2
5.7.3
5.8
5.9
5.9.1
PDBECHEM
PAGES
158
LIGAND-RELATED
ANNOTATIONS
IN
THE
PDBE-KB
158
INTRODUCTION
TO
PDBE-KB
158
DATA
ACCESS
MECHANISMS
FOR
LIGAND-RELATED
ANNOTATIONS
160
LIGAND-RELATED
ANNOTATIONS
ON
THE
AGGREGATED
VIEWS
OF
PROTEINS
162
CASE
STUDY:
USING
PDB
DATA
TO
SUPPORT
DRUG
DISCOVERY
164
CONCLUSIONS
AND
OUTLOOK
165
UPCOMING
FEATURES
AND
IMPROVEMENTS
166
REFERENCES
167
6
THE
SWISS-MODEL
REPOSITORY
OF
3D
PROTEIN
STRUCTURES
AND
MODELS
175
XAVIER
ROBIN,
ANDREW
MARK
WATERHOUSE,
STEFAN
BIENERT,
GABRIEL
STUDER,
LEILA
T.
ALEXANDER,
GERARDO
TAURIELLO,
TORSTEN
SCHWEDE,
AND
JOANA
PEREIRA
6.1
6.2
6.2.1
6.2.2
6.2.3
6.2.4
6.3
INTRODUCTION
175
SMR
DATABASE
CONTENT
AND
MODEL
PROVIDERS
176
PDB
177
SWISS-MODEL
177
ALPHAFOLD
DATABASE
179
MODELARCHIVE
180
PROTEIN
FEATURE
ANNOTATION
AND
CROSS-REFERENCES
TO
COMPUTATIONAL
RESOURCES
181
6.3.1
6.3.2
6.3.3
6.4
6.5
6.6
6.7
STRUCTURAL
FEATURES,
LIGANDS,
AND
OLIGOMERS
181
SWISS-MODEL
ASSOCIATED
TOOLS
182
WEB
AND
API
ACCESS
183
QUALITY
ESTIMATES
AND
BENCHMARKING
188
BINDING
SITE
CONFORMATIONAL
STATES
189
SMR
AND
COMPUTER-AIDED
STRUCTURE-BASED
DRUG
DESIGN
190
CONCLUSION
AND
OUTLOOK
191
REFERENCES
193
7
PDB-REDO
IN
COMPUTATIONAL-AIDED
DRUG
DESIGN
(CADD)
201
IDA
DE
VRIES,
ANASTASSIS
PERRAKIS,
AND
ROBBIE
P.
JOOSTEN
7.1
7.1.1
7.1.2
7.1.2.1
7.1.2.2
7.1.2.3
7.1.2.4
7.1.2.5
7.2
7.2.1
7.2.1.1
7.2.1.2
HISTORY
AND
CONCEPTS
201
X-RAY
STRUCTURE
MODELS
201
PDB-REDO
DEVELOPMENT
202
FIRST
UNIFORMITY
203
AUTOMATIC
REBUILDING
OF
PROTEIN
BACKBONE
AND
SIDE
CHAINS
203
AUTOMATED
MODEL
COMPLETION
APPROACHES
204
SYSTEMATIC
INTEGRATION
OF
STRUCTURAL
KNOWLEDGE
205
OVERVIEW
OF
PDB-REDO
PIPELINE
205
STRUCTURE
IMPROVEMENTS
BY
PDB-REDO
206
PARAMETRIZATION
AND
REBUILDING
EFFECTS
ON
SMALL
MOLECULE
LIGANDS
206
RE-REFINEMENT
IMPROVES
LIGAND
CONFORMATION
206
SIDE
CHAIN
REBUILDING
IMPROVES
LIGAND
BINDING
SITES
207
CONTENTS
IX
7.2.1.3
HISTIDINE
FLIP
AND
IMPROVED
LIGAND
PARAMETERIZATION
208
7.2.2
BUILDING
OF
PROTEIN
LOOPS
AND
LIGANDS
INTO
PROTEIN
STRUCTURE
MODELS
210
7.2.2.1
LOOP
BUILDING
COMPLETES
A
BINDING
SITE
REGION
210
7.2.2.2
LOOP
BUILDING
RESULTS
IN
IMPROVED
BINDING
SITES
211
7.2.2.3
BUILDING
NEW
COMPOUNDS
INTO
DENSITY
212
7.2.3
NUCLEIC
ACID
IMPROVEMENTS
BY
PDB-REDO
213
7.2.4
GLYCOPROTEIN
STRUCTURE
MODEL
REBUILDING
214
7.2.5
METAL
BINDING
SITES
214
7.2.6
LIMITATIONS
OF
THE
PDB-REDO
DATABANK
216
7.3
ACCESS
THE
PDB-REDO
DATABANK
AND
METADATA
218
7.3.1
DOWNLOADING
AND
INSPECTING
INDIVIDUAL
PDB-REDO
ENTRIES
218
7.3.2
DATA
AVAILABLE
IN
PDB-REDO
ENTRIES
220
7.3.3
USAGE
OF
THE
UNIFORM
AND
FAIR
VALIDATION
DATA
220
7.3.4
CREATING
DATASETS
FROM
THE
PDB-REDO
DATABANK
222
7.3.5
SUBMITTING
STRUCTURE
MODELS
TO
THE
PDB-REDO
PIPELINE
223
7.4
CONCLUSIONS
223
ACKNOWLEDGMENTS
AND
FUNDING
224
LIST
OF
ABBREVIATIONS
AND
SYMBOLS
224
REFERENCES
225
8
PHAROS
AND
TCRD:
INFORMATICS
TOOLS
FOR
ILLUMINATING
DARK
TARGETS
231
KEITH
J.
KELLEHER,
TIMOTHY
K.
SHEILS,
STEPHEN
L.
MATHIAS,
DAC-TRUNG
NGUYEN,
VISHAL
SIRAMSHETTY,
AJAY
PILLAI,
JEREMY
J.
YANG,
CRISTIAN
G.
BOLOGA,
JEREMY
S.
EDWARDS,
TUDOR
I.
OPREA,
AND
EWY
MATHE
8.1
INTRODUCTION
231
8.2
METHODS
233
8.2.1
DATA
ORGANIZATION
233
8.2.1.1
TARGET
ALIGNMENT
234
8.2.1.2
DISEASE
ALIGNMENT
234
8.2.1.3
LIGAND
ALIGNMENT
234
8.2.1.4
DATA
AND
UI
UPDATES
235
8.2.2
PROGRAMMATIC
ACCESS
AND
DATA
DOWNLOAD
235
8.2.3
UI
ORGANIZATION
235
8.2.3.1
LIST
PAGES
236
8.2.3.2
DETAILS
PAGES
236
8.2.3.3
SEARCH
238
8.2.3.4
TUTORIALS
240
8.2.4
ANALYSIS
METHODS
WITHIN
PHAROS
240
8.2.4.1
SEARCHING
FOR
LIGANDS
240
8.2.4.2
FINDING
TARGETS
BY
AMINO
ACID
SEQUENCE
241
8.2.4.3
FINDING
TARGETS
WITH
SIMILAR
ANNOTATIONS
241
8.2.4.4
FINDING
TARGETS
WITH
PREDICTED
ACTIVITY
241
8.2.4.5
ENRICHMENT
SCORES
FOR
FILTER
VALUES
241
CONTENTS
8.3
USE
CASES
242
8.3.1
HYPOTHESIZING
THE
ROLE
OF
A
DARK
TARGET
242
8.3.1.1
PRIMARY
DOCUMENTATION
242
8.3.1.2
LIST
ANALYSIS
247
8.3.1.3
DOWNLOADING
DATA
251
8.3.1.4
VARIATIONS
ON
THIS
USE
CASE
251
8.3.2
CHARACTERIZING A
NOVEL
CHEMICAL
COMPOUND
251
8.3.2.1
FINDING
PREDICTED
TARGETS
252
8.3.2.2
ANALYZING
SIMILAR
LIGANDS
254
8.3.2.3
LIGAND
DETAILS
PAGES
256
8.3.2.4
VARIATIONS
ON
THIS
USE
CASE
257
8.3.3
INVESTIGATING
DISEASES
260
8.4
DISCUSSION
262
FUNDING
264
REFERENCES
264
PARTLLL
USERS
'
POINTS
OF
VIEW
269
9
MINING
FOR
BIOACTIVE
MOLECULES
IN
OPEN
DATABASES
271
GUILLEM
MACIP,
JULIA
MESTRES-TRUYOL,
POL
GARCIA-SEGURA,
BRYAN
SALDIVAR-ESPINOZA,
SANTIAGO
GARCIA-VALLVE,
AND
GERARD
PUJADAS
9.1
INTRODUCTION
271
9.2
MAIN
TOOLS
FOR
VIRTUAL
SCREENING
272
9.2.1
ADMET
AND
PAINS
FILTERING
272
9.2.2
PROTEIN-LIGAND
DOCKING
274
9.2.3
PHARMACOPHORE
SEARCH
275
9.2.4
SHAPE/ELECTROSTATIC
SIMILARITY
276
9.2.5
PROTEIN-STRUCTURE
DATABASES
277
9.2.6
THE
PROTEIN
DATA
BANK
278
9.2.7
THE
PDB-REDO
DATABANK
278
9.2.8
THE
SWISS-MODEL
REPOSITORY
279
9.2.9
THE
ALPHAFOLD
PROTEIN
STRUCTURE
DATABASE
279
9.3
VALIDATING
BINDING
SITE
AND
LIGAND
COORDINATES
IN
THREE-DIMENSIONAL
PROTEIN
COMPLEXES
280
9.4
DATABASES
FOR
SEARCHING
NEW
DRUGS
281
9.4.1
COCONUT
281
9.4.2
GDBS
282
9.4.3
ZINC20
282
9.5
DATABASES
OF
BIOACTIVE
MOLECULES
282
9.5.1
THE
BINDINGDB
DATABASE
283
9.5.2
PUBCHEM
283
9.5.3
CHEMBL
284
9.6
DATABASES
OF
INACTIVE/DECOY
MOLECULES
285
CONTENTS
XI
9.6.1
9.6.2
9.6.3
9.7
9.8
COLLECTING
EXPERIMENTALLY
INACTIVE
COMPOUNDS
FROM
PUBCHEM
285
COLLECTING
PRESUMED
INACTIVE
COMPOUNDS
FROM
DECOY
DATABASES
285
BUILDING
CUSTOM-BASED
DECOY
SETS
286
MAIN
METRICS
FOR
EVALUATING
THE
SUCCESS
OF
A
VIRTUAL
SCREENING
286
CONCLUDING
REMARKS
288
REFERENCES
289
10
OPEN
ACCESS
DATABASES
-
AN
INDUSTRIAL
VIEW
299
MICHAEL
PRZEWOSNY
10.1
10.2
10.3
ACADEMIC
VS.
INDUSTRIAL
RESEARCH
299
SCAFFOLD-HOPPING
310
VIRTUAL-SCREENING
311
ABBREVIATIONS
312
REFERENCES
313
INDEX
317 |
| adam_txt |
CONTENTS
SERIES
EDITORS
PREFACE
XIII
RAIMUND
MANNHOLD
-
A
PERSONAL
OBITUARY
FROM
THE
SERIES
EDITORS
XVII
A
PERSONAL
FOREWORD
XXI
1
OPEN
ACCESS
DATABASES
AND
DATASETS
FOR
COMPUTER-AIDED
DRUG
DESIGN.
A
SHORT
LIST
USED
IN
THE
MOLECULAR
MODELLING
GROUP
OF
THE
SIB
1
ANTOINE
DAINA,
MARIA
JOSE
OJEDA-MONTES,
MAIIA
E.
BRAGINA,
ALESSANDRO
CUOZZO,
UTE
F.
ROHRIG,
MARTA
A.S.
PEREZ,
AND
VINCENT
ZOETE
REFERENCES
30
PART
I
SMALL
MOLECULES
39
2
PUBCHEM:
A
LARGE-SCALE
PUBLIC
CHEMICAL
DATABASE
FOR
DRUG
DISCOVERY
41
SUNGHWAN
KIM
AND
EVAN
E.
BOLTON
2.1
INTRODUCTION
41
2.2
DATA
CONTENT
AND
ORGANIZATION
42
2.3
TOOLS
AND
SERVICES
45
2.3.1
PUBCHEM
SEARCH
45
2.3.2
SUMMARY
PAGES
48
2.3.3
LITERATURE
KNOWLEDGE
PANEL
49
2.3.4
2D
AND
3D
NEIGHBORS
50
2.3.5
CLASSIFICATION
BROWSER
51
2.3.6
IDENTIFIER
EXCHANGE
SERVICE
52
2.3.7
PROGRAMMATIC
ACCESS
52
2.3.8
PUBCHEM
FTP
SITE
AND
PUBCHEMRDF
53
2.4
DRUG
AND
LEAD-LIKENESS
OF
PUBCHEM
COMPOUNDS
54
2.5
BIOACTIVITY
DATA
IN
PUBCHEM
56
2.6
COMPARISON
WITH
OTHER
DATABASES
57
2.7
USE
OF
PUBCHEM
DATA
FOR
DRUG
DISCOVERY
58
2.8
SUMMARY
59
ACKNOWLEDGMENTS
60
REFERENCES
60
VI
CONTENTS
3
DRUGBANK
ONLINE:
A
HOW-TO
GUIDE
67
CHRISTEN
M.
KLINGER,
JORDAN
COX,
DENISE
SO,
TEIRA
STAUTH,
MICHAEL
WILSON,
ALEX
WILSON,
AND
CRAIG
KNOX
3.1
3.2
3.2.1
3.2.2
3.2.2.1
3.2.2.2
3.2.2.3
3.2.2.4
3.2.2.5
3.2.2.6
3.2.2.7
3.3
3.3.1
3.3.1.1
3.3.1.2
3.3.1.3
3.3.2
3.3.2.1
3.3.2.2
3.3.3
3.4
3.5
INTRODUCTION
67
DRUGBANK
68
OVERVIEW
OF
DRUGBANK
68
DRUGBANK
DATASETS
69
DRUG
CARDS:
AN
OVERVIEW
AND
NAVIGATION
GUIDE
70
IDENTIFICATION
70
PHARMACOLOGY
71
CATEGORIES
73
PROPERTIES
73
TARGETS,
ENZYMES,
CARRIERS,
AND
TRANSPORTERS
73
REFERENCES
77
PROTOCOLS
77
GENERAL
WORKFLOWS
77
USING
DRUGBANK
ONLINE
'
S
SEARCH
FUNCTIONALITY
77
USING
DRUGBANK
ONLINE
'
S
ADVANCED
SEARCH
FUNCTIONALITY
80
BROWSING
DRUGS
USING
DRUGBANK
ONLINE
'
S
DRUG
CATEGORIES
83
IDENTIFYING
CHEMICALS
AND
RELEVANT
SEQUENCES
86
SEARCHING
USING
CHEMICAL
STRUCTURE
SEARCH
86
USING
SEQUENCE
SEARCH
TO
FIND
SIMILAR
TARGETS
89
EXTRACTING
DRUGBANK
DATASETS
FOR
ML
93
RESEARCH
USING
DRUGBANK
94
DISCUSSION
AND
CONCLUSIONS
95
REFERENCES
96
4
BIOISOSTERIC
REPLACEMENT
FOR
DRUG
DISCOVERY
SUPPORTED
BY
THE
SWISSBIOISOSTERE
DATABASE
101
ANTOINE
DAINA,
ALESSANDRO
CUOZZO,
MARTA
A.S.
PEREZ,
AND
VINCENT
ZOETE
4.1
4.1.1
4.1.2
INTRODUCTION
101
CONCEPT
OF
ISOSTERISM
AND
BIOISOSTERISM
101
CLASSICAL
VS.
NON-CLASSICAL
BIOISOSTERE
AND
FURTHER
MOLECULAR
REPLACEMENTS
102
4.1.3
4.2
4.2.1
4.2.2
4.2.3
4.2.4
4.2.5
4.3
4.3.1
4.3.2
4.3.3
BIOISOSTERIC
REPLACEMENT
IN
DRUG
DISCOVERY
105
CONSTRUCTION
AND
DISSEMINATION
OF
SWISSBIOISOSTERE
106
INTENTION
AND
REQUIREMENTS
106
BIOACTIVITY
DATA
107
NONSUPERVISED
MATCHED
MOLECULAR
PAIR
ANALYSIS
108
DATABASE
108
WEB
INTERFACE
109
CONTENT
OF
SWISSBIOISOSTERE
111
GLOBAL
CONTENT
111
BIOLOGICAL
AND
CHEMICAL
CONTEXTS
112
FRAGMENT
SHAPE
DIVERSITY
113
CONTENTS
VII
4.4
USAGE
OF
SWISSBIOISOSTERE
115
4.4.1
WEBSITE USAGE
115
4.4.2
MOST
FREQUENT
REQUESTS
117
4.4.3
EXAMPLES
RELATED
TO
DRUG
DISCOVERY
117
4.4.3.1
USE
CASES
117
4.4.3.2
REPLACING
UNWANTED
CHEMICAL
GROUPS
118
4.4.3.3
OPTIMIZATION
OF
PASSIVE
ABSORPTION
AND
BLOOD-BRAIN
BARRIER
DIFFUSION
122
4.4.3.4
REDUCTION
OF
FLEXIBILITY
124
4.4.3.5
REDUCTION
OF
AROMATICITY/ESCAPE
FROM
FLATLAND
128
4.5
CONCLUSIVE
REMARKS
133
ACKNOWLEDGMENT
133
REFERENCES
133
PART
II
MACROMOLECULAR
TARGETS
AND
DISEASES
139
5
THE
PROTEIN
DATA
BANK
(PDB)
AND
MACROMOLECULAR
STRUCTURE
DATA
SUPPORTING
COMPUTER-AIDED
DRUG
DESIGN
141
DAVID
ARMSTRONG,
JOHN
BERRISFORD,
PREETI
CHOUDHARY,
LUKAS
PRAVDA,
JAMES
TOLCHARD,
MIHOLY
VARADI,
AND
SAMEER
VELANKAR
5.1
INTRODUCTION
141
5.2
SMALL
MOLECULE
DATA
IN
PROTEIN
DATA
BANK
(PDB)
ENTRIES
142
5.2.1
WHAT
DATA
ARE
IN
THE
PDB
ARCHIVE?
142
5.2.2
DEFINITION
OF
SMALL
MOLECULES
IN
ONEDEP
145
5.3
SMALL
MOLECULE
DICTIONARIES
146
5.3.1
WWPDB
CHEMICAL
COMPONENT
DICTIONARY
(CCD)
146
5.3.2
THE
PEPTIDE
REFERENCE
DICTIONARY
147
5.4
ADDITIONAL
LIGAND
ANNOTATIONS
IN
THE
PDB
ARCHIVE
148
5.4.1
LINKAGE
INFORMATION
148
5.4.2
CARBOHYDRATES
149
5.5
VALIDATION
OF
LIGANDS
IN
THE
WORLDWIDE
PROTEIN
DATA
BANK
(WWPDB)
150
5.5.1
VARIOUS
CRITERIA
AND
SOFTWARE
USED
FOR
VALIDATING
LIGAND
IN
VALIDATION
REPORTS
150
5.5.2
IDENTIFICATION
OF
LIGAND
OF
INTEREST
(LOI)
151
5.5.3
GEOMETRIC
AND
CONFORMATIONAL
VALIDATION
152
5.5.4
LIGAND
FIT
TO
EXPERIMENTAL
ELECTRON
DENSITY
VALIDATION
152
5.5.5
ACCESSING
WWPDB
VALIDATION
REPORTS
FROM
PDBE
ENTRY
PAGES
154
5.5.6
OTHER
PLANNED
IMPROVEMENTS
TO
ENHANCE
LIGAND
VALIDATION
154
5.6
PDBE
TOOLS
FOR
LIGAND
ANALYSIS
155
5.6.1
LIGAND
INTERACTIONS
155
5.6.1.1
CLASSIFYING
LIGAND
INTERACTIONS
155
5.6.1.2
DATA
AVAILABILITY
156
5.6.2
LIGAND
ENVIRONMENT
COMPONENT
156
5.6.3
CHEMISTRY
PROCESS
AND
FTP
158
VIII
CONTENTS
5.6.4
5.7
5.7.1
5.7.2
5.7.3
5.8
5.9
5.9.1
PDBECHEM
PAGES
158
LIGAND-RELATED
ANNOTATIONS
IN
THE
PDBE-KB
158
INTRODUCTION
TO
PDBE-KB
158
DATA
ACCESS
MECHANISMS
FOR
LIGAND-RELATED
ANNOTATIONS
160
LIGAND-RELATED
ANNOTATIONS
ON
THE
AGGREGATED
VIEWS
OF
PROTEINS
162
CASE
STUDY:
USING
PDB
DATA
TO
SUPPORT
DRUG
DISCOVERY
164
CONCLUSIONS
AND
OUTLOOK
165
UPCOMING
FEATURES
AND
IMPROVEMENTS
166
REFERENCES
167
6
THE
SWISS-MODEL
REPOSITORY
OF
3D
PROTEIN
STRUCTURES
AND
MODELS
175
XAVIER
ROBIN,
ANDREW
MARK
WATERHOUSE,
STEFAN
BIENERT,
GABRIEL
STUDER,
LEILA
T.
ALEXANDER,
GERARDO
TAURIELLO,
TORSTEN
SCHWEDE,
AND
JOANA
PEREIRA
6.1
6.2
6.2.1
6.2.2
6.2.3
6.2.4
6.3
INTRODUCTION
175
SMR
DATABASE
CONTENT
AND
MODEL
PROVIDERS
176
PDB
177
SWISS-MODEL
177
ALPHAFOLD
DATABASE
179
MODELARCHIVE
180
PROTEIN
FEATURE
ANNOTATION
AND
CROSS-REFERENCES
TO
COMPUTATIONAL
RESOURCES
181
6.3.1
6.3.2
6.3.3
6.4
6.5
6.6
6.7
STRUCTURAL
FEATURES,
LIGANDS,
AND
OLIGOMERS
181
SWISS-MODEL
ASSOCIATED
TOOLS
182
WEB
AND
API
ACCESS
183
QUALITY
ESTIMATES
AND
BENCHMARKING
188
BINDING
SITE
CONFORMATIONAL
STATES
189
SMR
AND
COMPUTER-AIDED
STRUCTURE-BASED
DRUG
DESIGN
190
CONCLUSION
AND
OUTLOOK
191
REFERENCES
193
7
PDB-REDO
IN
COMPUTATIONAL-AIDED
DRUG
DESIGN
(CADD)
201
IDA
DE
VRIES,
ANASTASSIS
PERRAKIS,
AND
ROBBIE
P.
JOOSTEN
7.1
7.1.1
7.1.2
7.1.2.1
7.1.2.2
7.1.2.3
7.1.2.4
7.1.2.5
7.2
7.2.1
7.2.1.1
7.2.1.2
HISTORY
AND
CONCEPTS
201
X-RAY
STRUCTURE
MODELS
201
PDB-REDO
DEVELOPMENT
202
FIRST
UNIFORMITY
203
AUTOMATIC
REBUILDING
OF
PROTEIN
BACKBONE
AND
SIDE
CHAINS
203
AUTOMATED
MODEL
COMPLETION
APPROACHES
204
SYSTEMATIC
INTEGRATION
OF
STRUCTURAL
KNOWLEDGE
205
OVERVIEW
OF
PDB-REDO
PIPELINE
205
STRUCTURE
IMPROVEMENTS
BY
PDB-REDO
206
PARAMETRIZATION
AND
REBUILDING
EFFECTS
ON
SMALL
MOLECULE
LIGANDS
206
RE-REFINEMENT
IMPROVES
LIGAND
CONFORMATION
206
SIDE
CHAIN
REBUILDING
IMPROVES
LIGAND
BINDING
SITES
207
CONTENTS
IX
7.2.1.3
HISTIDINE
FLIP
AND
IMPROVED
LIGAND
PARAMETERIZATION
208
7.2.2
BUILDING
OF
PROTEIN
LOOPS
AND
LIGANDS
INTO
PROTEIN
STRUCTURE
MODELS
210
7.2.2.1
LOOP
BUILDING
COMPLETES
A
BINDING
SITE
REGION
210
7.2.2.2
LOOP
BUILDING
RESULTS
IN
IMPROVED
BINDING
SITES
211
7.2.2.3
BUILDING
NEW
COMPOUNDS
INTO
DENSITY
212
7.2.3
NUCLEIC
ACID
IMPROVEMENTS
BY
PDB-REDO
213
7.2.4
GLYCOPROTEIN
STRUCTURE
MODEL
REBUILDING
214
7.2.5
METAL
BINDING
SITES
214
7.2.6
LIMITATIONS
OF
THE
PDB-REDO
DATABANK
216
7.3
ACCESS
THE
PDB-REDO
DATABANK
AND
METADATA
218
7.3.1
DOWNLOADING
AND
INSPECTING
INDIVIDUAL
PDB-REDO
ENTRIES
218
7.3.2
DATA
AVAILABLE
IN
PDB-REDO
ENTRIES
220
7.3.3
USAGE
OF
THE
UNIFORM
AND
FAIR
VALIDATION
DATA
220
7.3.4
CREATING
DATASETS
FROM
THE
PDB-REDO
DATABANK
222
7.3.5
SUBMITTING
STRUCTURE
MODELS
TO
THE
PDB-REDO
PIPELINE
223
7.4
CONCLUSIONS
223
ACKNOWLEDGMENTS
AND
FUNDING
224
LIST
OF
ABBREVIATIONS
AND
SYMBOLS
224
REFERENCES
225
8
PHAROS
AND
TCRD:
INFORMATICS
TOOLS
FOR
ILLUMINATING
DARK
TARGETS
231
KEITH
J.
KELLEHER,
TIMOTHY
K.
SHEILS,
STEPHEN
L.
MATHIAS,
DAC-TRUNG
NGUYEN,
VISHAL
SIRAMSHETTY,
AJAY
PILLAI,
JEREMY
J.
YANG,
CRISTIAN
G.
BOLOGA,
JEREMY
S.
EDWARDS,
TUDOR
I.
OPREA,
AND
EWY
MATHE
8.1
INTRODUCTION
231
8.2
METHODS
233
8.2.1
DATA
ORGANIZATION
233
8.2.1.1
TARGET
ALIGNMENT
234
8.2.1.2
DISEASE
ALIGNMENT
234
8.2.1.3
LIGAND
ALIGNMENT
234
8.2.1.4
DATA
AND
UI
UPDATES
235
8.2.2
PROGRAMMATIC
ACCESS
AND
DATA
DOWNLOAD
235
8.2.3
UI
ORGANIZATION
235
8.2.3.1
LIST
PAGES
236
8.2.3.2
DETAILS
PAGES
236
8.2.3.3
SEARCH
238
8.2.3.4
TUTORIALS
240
8.2.4
ANALYSIS
METHODS
WITHIN
PHAROS
240
8.2.4.1
SEARCHING
FOR
LIGANDS
240
8.2.4.2
FINDING
TARGETS
BY
AMINO
ACID
SEQUENCE
241
8.2.4.3
FINDING
TARGETS
WITH
SIMILAR
ANNOTATIONS
241
8.2.4.4
FINDING
TARGETS
WITH
PREDICTED
ACTIVITY
241
8.2.4.5
ENRICHMENT
SCORES
FOR
FILTER
VALUES
241
CONTENTS
8.3
USE
CASES
242
8.3.1
HYPOTHESIZING
THE
ROLE
OF
A
DARK
TARGET
242
8.3.1.1
PRIMARY
DOCUMENTATION
242
8.3.1.2
LIST
ANALYSIS
247
8.3.1.3
DOWNLOADING
DATA
251
8.3.1.4
VARIATIONS
ON
THIS
USE
CASE
251
8.3.2
CHARACTERIZING A
NOVEL
CHEMICAL
COMPOUND
251
8.3.2.1
FINDING
PREDICTED
TARGETS
252
8.3.2.2
ANALYZING
SIMILAR
LIGANDS
254
8.3.2.3
LIGAND
DETAILS
PAGES
256
8.3.2.4
VARIATIONS
ON
THIS
USE
CASE
257
8.3.3
INVESTIGATING
DISEASES
260
8.4
DISCUSSION
262
FUNDING
264
REFERENCES
264
PARTLLL
USERS
'
POINTS
OF
VIEW
269
9
MINING
FOR
BIOACTIVE
MOLECULES
IN
OPEN
DATABASES
271
GUILLEM
MACIP,
JULIA
MESTRES-TRUYOL,
POL
GARCIA-SEGURA,
BRYAN
SALDIVAR-ESPINOZA,
SANTIAGO
GARCIA-VALLVE,
AND
GERARD
PUJADAS
9.1
INTRODUCTION
271
9.2
MAIN
TOOLS
FOR
VIRTUAL
SCREENING
272
9.2.1
ADMET
AND
PAINS
FILTERING
272
9.2.2
PROTEIN-LIGAND
DOCKING
274
9.2.3
PHARMACOPHORE
SEARCH
275
9.2.4
SHAPE/ELECTROSTATIC
SIMILARITY
276
9.2.5
PROTEIN-STRUCTURE
DATABASES
277
9.2.6
THE
PROTEIN
DATA
BANK
278
9.2.7
THE
PDB-REDO
DATABANK
278
9.2.8
THE
SWISS-MODEL
REPOSITORY
279
9.2.9
THE
ALPHAFOLD
PROTEIN
STRUCTURE
DATABASE
279
9.3
VALIDATING
BINDING
SITE
AND
LIGAND
COORDINATES
IN
THREE-DIMENSIONAL
PROTEIN
COMPLEXES
280
9.4
DATABASES
FOR
SEARCHING
NEW
DRUGS
281
9.4.1
COCONUT
281
9.4.2
GDBS
282
9.4.3
ZINC20
282
9.5
DATABASES
OF
BIOACTIVE
MOLECULES
282
9.5.1
THE
BINDINGDB
DATABASE
283
9.5.2
PUBCHEM
283
9.5.3
CHEMBL
284
9.6
DATABASES
OF
INACTIVE/DECOY
MOLECULES
285
CONTENTS
XI
9.6.1
9.6.2
9.6.3
9.7
9.8
COLLECTING
EXPERIMENTALLY
INACTIVE
COMPOUNDS
FROM
PUBCHEM
285
COLLECTING
PRESUMED
INACTIVE
COMPOUNDS
FROM
DECOY
DATABASES
285
BUILDING
CUSTOM-BASED
DECOY
SETS
286
MAIN
METRICS
FOR
EVALUATING
THE
SUCCESS
OF
A
VIRTUAL
SCREENING
286
CONCLUDING
REMARKS
288
REFERENCES
289
10
OPEN
ACCESS
DATABASES
-
AN
INDUSTRIAL
VIEW
299
MICHAEL
PRZEWOSNY
10.1
10.2
10.3
ACADEMIC
VS.
INDUSTRIAL
RESEARCH
299
SCAFFOLD-HOPPING
310
VIRTUAL-SCREENING
311
ABBREVIATIONS
312
REFERENCES
313
INDEX
317 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author2 | Daina, Antoine Przewosny, Michael Thomas 1958- Zoete, Vincent |
| author2_role | edt edt edt |
| author2_variant | a d ad m t p mt mtp v z vz |
| author_GND | (DE-588)1311338039 (DE-588)172738520 (DE-588)1311339396 |
| author_facet | Daina, Antoine Przewosny, Michael Thomas 1958- Zoete, Vincent |
| building | Verbundindex |
| bvnumber | BV049357911 |
| classification_rvk | VC 6700 VS 5350 |
| ctrlnum | (OCoLC)1411117861 (DE-599)DNB1285617355 |
| discipline | Chemie / Pharmazie |
| discipline_str_mv | Chemie / Pharmazie |
| format | Book |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV049357911 |
| illustrated | Illustrated |
| index_date | 2024-07-03T22:51:40Z |
| indexdate | 2024-08-27T00:08:06Z |
| institution | BVB |
| institution_GND | (DE-588)16179388-5 |
| isbn | 3527348395 9783527348398 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-034618104 |
| oclc_num | 1411117861 |
| open_access_boolean | |
| owner | DE-29T DE-703 DE-20 DE-19 DE-BY-UBM |
| owner_facet | DE-29T DE-703 DE-20 DE-19 DE-BY-UBM |
| physical | xxi, 323 Seiten Illustrationen, Diagramme 24.4 cm x 17 cm |
| publishDate | 2024 |
| publishDateSearch | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley-VCH |
| record_format | marc |
| series | Methods and principles in medicinal chemistry |
| series2 | Methods and principles in medicinal chemistry |
| spelling | Open access databases and datasets for drug discovery edited by Antoine Daina, Michael Przewosny, and Vincent Zoete Weinheim, Germany Wiley-VCH [2024] xxi, 323 Seiten Illustrationen, Diagramme 24.4 cm x 17 cm txt rdacontent n rdamedia nc rdacarrier Methods and principles in medicinal chemistry volume 83 Arzneimittelentwicklung (DE-588)4143176-5 gnd rswk-swf Open Access (DE-588)7525775-0 gnd rswk-swf Faktendatenbank (DE-588)4212429-3 gnd rswk-swf Arzneimittelforschung (DE-588)4003120-2 gnd rswk-swf Biowissenschaften CH61: Wirkstoffforschung u. -entwicklung CHD0: Computational Chemistry u. Molecular Modeling Chemie Chemistry Computational Chemistry & Molecular Modeling Computational Chemistry u. Molecular Modeling Drug Discovery & Development LS38: Strukturbiologie Life Sciences Structural Biology Strukturbiologie Wirkstoffforschung Wirkstoffforschung u. -entwicklung (DE-588)4143413-4 Aufsatzsammlung gnd-content Arzneimittelentwicklung (DE-588)4143176-5 s Faktendatenbank (DE-588)4212429-3 s Open Access (DE-588)7525775-0 s DE-604 Arzneimittelforschung (DE-588)4003120-2 s Daina, Antoine (DE-588)1311338039 edt Przewosny, Michael Thomas 1958- (DE-588)172738520 edt Zoete, Vincent (DE-588)1311339396 edt Wiley-VCH (DE-588)16179388-5 pbl Erscheint auch als Online-Ausgabe, PDF 978-3-527-83047-3 Erscheint auch als Online-Ausgabe, EPUB 978-3-527-83048-0 Erscheint auch als Online-Ausgabe, oBook 978-3-527-83049-7 Methods and principles in medicinal chemistry volume 83 (DE-604)BV035418617 83 X:MVB http://www.wiley-vch.de/publish/dt/books/ISBN978-3-527-34839-8/ DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034618104&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p vlb 20230406 DE-101 https://d-nb.info/provenance/plan#vlb |
| spellingShingle | Open access databases and datasets for drug discovery Methods and principles in medicinal chemistry Arzneimittelentwicklung (DE-588)4143176-5 gnd Open Access (DE-588)7525775-0 gnd Faktendatenbank (DE-588)4212429-3 gnd Arzneimittelforschung (DE-588)4003120-2 gnd |
| subject_GND | (DE-588)4143176-5 (DE-588)7525775-0 (DE-588)4212429-3 (DE-588)4003120-2 (DE-588)4143413-4 |
| title | Open access databases and datasets for drug discovery |
| title_auth | Open access databases and datasets for drug discovery |
| title_exact_search | Open access databases and datasets for drug discovery |
| title_exact_search_txtP | Open access databases and datasets for drug discovery |
| title_full | Open access databases and datasets for drug discovery edited by Antoine Daina, Michael Przewosny, and Vincent Zoete |
| title_fullStr | Open access databases and datasets for drug discovery edited by Antoine Daina, Michael Przewosny, and Vincent Zoete |
| title_full_unstemmed | Open access databases and datasets for drug discovery edited by Antoine Daina, Michael Przewosny, and Vincent Zoete |
| title_short | Open access databases and datasets for drug discovery |
| title_sort | open access databases and datasets for drug discovery |
| topic | Arzneimittelentwicklung (DE-588)4143176-5 gnd Open Access (DE-588)7525775-0 gnd Faktendatenbank (DE-588)4212429-3 gnd Arzneimittelforschung (DE-588)4003120-2 gnd |
| topic_facet | Arzneimittelentwicklung Open Access Faktendatenbank Arzneimittelforschung Aufsatzsammlung |
| url | http://www.wiley-vch.de/publish/dt/books/ISBN978-3-527-34839-8/ http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034618104&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035418617 |
| work_keys_str_mv | AT dainaantoine openaccessdatabasesanddatasetsfordrugdiscovery AT przewosnymichaelthomas openaccessdatabasesanddatasetsfordrugdiscovery AT zoetevincent openaccessdatabasesanddatasetsfordrugdiscovery AT wileyvch openaccessdatabasesanddatasetsfordrugdiscovery |