Bioinformation discovery: data to knowledge in biology
Gespeichert in:
1. Verfasser: | |
---|---|
Format: | Buch |
Sprache: | English |
Veröffentlicht: |
New York, NY [u.a.]
Springer
2009
|
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | XXV, 166 S. Ill., graph. Darst. |
ISBN: | 9781441905185 |
Internformat
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Datensatz im Suchindex
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---|---|
adam_text | Contents
1
Introduction
............................................................................................... 1
1.1
Bioinformatícs
.................................................................................. 1
1.2 Bioinformatics-Related
Terms
......................................................... 2
1.3
Journals Supporting Bioinformatics
................................................ 2
1.4
Bioinformatics in Drug Discovery
................................................... 4
1.5
Skills for Bioinformatics
.................................................................. 4
1.6
Bioinformatics Warehousing in Drug Discovery
............................. 5
1.7
Bioinformatics Components
............................................................ 5
1.8 Bioinformation................................................................................. 6
1.9
Bioinformatics Variables
.................................................................. 7
1.10
Cell Constituents
.............................................................................. 7
1.10.1
Nucleic Acids
..................................................................... 8
1.10.2
Proteins
.............................................................................. 9
1.10.3
Classification of
Amino
Acids
........................................... 9
1
Л
I Codon and Codon Usage Table
........................................................ 9
1.12 Bioinformation
Discovery
................................................................ 11
1.13
Bioinformatics Principle
.................................................................. 11
1.14
Bioinformatics Challenges
............................................................... 12
1.15
Biological Data
................................................................................ 12
1.16
Data Explosion
................................................................................. 14
1.17
Sequence Data
.................................................................................. 14
1.18
Structure Data
.................................................................................. 14
1.19
Small Molecules
............................................................................... 14
1.20
Macromolecules
............................................................................... 16
1.21
SCOP
Dataset
................................................................................... 17
1.22
CATH
Dataset
.................................................................................. 18
1.23
Function Data
................................................................................... 20
1.24
Pathways Data
....................................................................·............. 20
1.25
Bioinformatics Developments
.......................................................... 21
1.26
Discovery Environment
........................................·.......................... 21
1.27
Sequence, Structure Alignment and Evolutionary
Inferences
..........................................·.............................................. 22
xi
xii
Contents
1.28
Molecular Modeling
......................................................................... 24
1.28.1
Protein Modeling
............................................................... 24
1.28.2
Methods of Protein Modeling
............................................ 25
1.28.3
Caveats on Homology Modeling
....................................... 26
1.29
Exercises
.......................................................................................... 26
2
Creating
Datasets
...................................................................................... 27
2.1
Datasets............................................................................................
27
2.2 HLA-Binding
Peptide Dataset
......................................................... 29
2.3
MHC-Peptide
Structural
Dataset
..................................................... 29
2.4
MHC-Peptide
Structure
Dataset Clustering
.................................... 32
2.5
PDB Chain
Identifier
....................................................................... 32
2.6
Information
Redundancy in
Dataset
................................................ 36
2.7
Information
from MHC-Peptide
Data
.............................................. 36
2.8
Structural
Parameters
for MHC-Peptide
Dataset
Analysis
............. 37
2.9
Creation
of Heterodimer and Homodimer Dataset
.......................... 37
2.10
Homodimer
Folding
Dataset
............................................................ 37
2.11
Alanine-Mutated Interface
Residues
Dataset
................................... 37
2.12
Intronless
Genes
Dataset
.................................................................. 59
2.13
Human
Single Exon Gene
(SEG)
Dataset
....................................... 61
2.14
Intron-Containing
Genes
Dataset
..................................................... 61
2.15
Fusion Protein
Dataset
..................................................................... 62
2.16
Exercises..........................................................................................
63
References
................................................................................................... 64
3
Tools and Techniques
................................................................................ 65
3.1
Align
................................................................................................ 65
3.2
BIMAS
............................................................................................. 66
3.3
BLAST
............................................................................................. 66
3.4
ClustalW
.......................................................................................... 68
3.5
DeCypher
......................................................................................... 69
3.6
DeepView
......................................................................................... 69
3.7
FASTA
.............................................................................................. 69
3.8
Insight II
........................................................................................... 69
3.9
Genscan
............................................................................................ 70
3.10
GROMOS
......................................................................................... 70
3.11
HBPLUS
.......................................................................................... 70
3.12
Lalign/Plalign
................................................................................... 71
3.13
Ligplot
.............................................................................................. 71
3.14
LOOK
.............................................................................................. 71
3.15
Modeller
........................................................................................... 72
3.16
NACCESS
........................................................................................ 73
3.17
Phylip
............................................................................................... 73
3.18
ProtParam
......................................................................................... 74
3.19
Protorp
.............................................................................................. 74
Contents
3.20
Psap
.................................................................................................. 74
3.21 Ppsearch........................................................................................... 74
3.22 Pymol............................................................................................... 74
3.23 Rasmol............................................................................................. 74
3.24
Rosetta
Design................................................................................. 75
3.25 Surfnet.............................................................................................. 75
3.26 Sybyl................................................................................................ 75
3.27 T-Epitope Designer.......................................................................... 75
3.28
Exercises
.......................................................................................... 75
References...................................................................................................
76
Protein Subunits
Interaction
.................................................................... 79
4.1 Protein
Subunit
Interaction..............................................................
79
4.2 Dimer Datasets in
Literature
............................................................ 80
4.3 Parameters in
Subunit
Interaction....................................................
81
4.3.1 Hydrophobie
Effect..............................................................
81
4.3.2 Interface
Size.......................................................................
82
4.3.3 Interface H-Bonds................................................................ 82
4.3.4 Interface
Residues
................................................................ 84
4.3.5 Interface
Residue Type
......................................................... 84
4.3.6
Inferences on
Protein
Subunit Interactions
.......................... 85
4.4
Exercises
.......................................................................................... 85
References
................................................................................................... 86
Homodinier
Folding and Binding
............................................................ 87
5.1
Importance of Homodimers
............................................................. 87
5.2
Homodimer Folding
......................................................................... 88
5.3
Homodimer Structures in Folding
................................................... 89
5.4
Size, Interface Area and Structure
................................................... 89
5.5
Interface to Total Residues
............................................................... 92
5.6
Exterior, Interior and Interface Hydrophobicity
in 2S and 3S
..................................................................................... 93
5.7
Folding and Binding Mechanism
..................................................... 94
5.8
Concluding Remarks
........................................................................ 96
5.9
Exercises
.......................................................................................... 96
References
................................................................................................... 96
Fusion Proteins
.......................................................................................... 97
6.1
Gene Fusion
..................................................................................... 97
6.2
Opérons
in Prokaryotes as Human Fusion Proteins
......................... 98
6.3
Multiple Functions in Fusion Proteins
............................................. 100
6.4
Alternative Splicing in Fusion Genes
.............................................. 101
6.5
Protein
Subunit
Interaction and Fusion Proteins
............................. 101
6.6
Mechanism of Gene Fusion
............................................................. 102
6.7
Hypothesis of Gene Fusion
.............................................................. 102
xjv Contents
6.8
Structural Importance of Fusion Proteins
........................................ 102
6.8.1
Fusion Protein IGPS Function
............................................. 103
6.8.2
Fusion Protein IGPS Structure
............................................. 104
6.8.3
IGPS Sequence, Structure and Properties
............................ 105
6.8.4
Interface Area in IGPS
......................................................... 106
6.8.5
Gap Volume in IGPS
............................................................ 106
6.8.6
Radius of Gyration in IGPS
................................................. 108
6.8.7
Structural Features of Fusion Protein IGPS
......................... 108
6.9
Exercises
.......................................................................................... 109
References
...................................................................................................
HO
7
Major Histocompatibility Complex (MHC)
and
Peptide
Binding
.................................................................................. 111
7.1
MHC Biology and Diversity
............................................................ 111
7.2
Promise of MHC in Medicine
.......................................................... 114
7.3
MHC Structure and Function
........................................................... 114
7.3.1
Class I MHC Structure and Function
................................... 115
7.3.2
Class II MHC Structure and Function
................................. 118
7.4
MHC-Peptide Motifs
....................................................................... 120
7.4.1
Class I MHC-Peptide Motifs
............................................... 120
7.4.2
Class II MHC-Peptide Motifs
.............................................. 121
7.5
MHC-Peptide Binding
..................................................................... 122
7.6
MHC Polymorphism and Specificity
............................................... 123
7.7
MHC-Peptide Complex in T-Cell-Mediated
Immune Response
............................................................................ 123
7.8
MHC-Peptide Binding Predictions
.................................................. 124
7.8.1
Data-Driven Methods
........................................................... 124
7.8.2
Molecular Modeling Methods
.............................................. 126
7.8.3
Limitations in Molecular Modeling Methods
...................... 127
7.9
Application
....................................................................................... 127
7.10
Exercises
.......................................................................................... 128
References
................................................................................................... 128
8
HLA
Supertypes........................................................................................
131
8.1
HLA
Supertypes:
Definition
............................................................ 131
8.2
Grouping of
HLA
Alíeles
by Several Research Groups
.................. 133
8.3
Perplexing Issues with
HLA
Supertypes.........................................
134
8.4
Structural Basis for
HLA
Supertypes..............................................
134
8.5
Predictive Grouping of
HLA
Supertypes.........................................
136
8.6
Grouping Using Electrostatic Distribution Maps
............................ 137
8.7
Concluding Remarks
........................................................................ 137
8.8
Exercises
.......................................................................................... 138
References
................................................................................................... 138
Contents xv
9 T-Epitope Designer................................................................................. 141
9.1 HLA-Peptide
Binding and Its Prediction.....................................
141
9.2
Available Prediction Servers
........................................................ 142
9.3
T-Epitope Designer
...................................................................... 142
9.4
Model
........................................................................................... 142
9.5
User Interface
............................................................................... 144
9.6
Input Data
..................................................................................... 144
9.7
Output Result
............................................................................... 145
9.8
Conclusion
................................................................................... 145
9.9
Cautionary Note
........................................................................... 145
9.10
Exercises
...................................................................................... 146
References
................................................................................................. 146
10
Eukaryotic Genes, Functions, Genomes,
Design, and Evolution
............................................................................. 149
10.1
Eukaryotic Genes and Genomes
.................................................. 149
10.2
SEGE
............................................................................................ 151
10.3
Genome
SEGE
............................................................................. 151
10.4
Human Single Exon Genes
.......................................................... 152
10.5
U-Genome
.................................................................................... 154
10.6
Exlnt
............................................................................................. 154
10.7
Alternative Splicing
..................................................................... 155
10.8
Intron
and Exon Content in Genomes
.......................................... 156
10.9
Exon-Intron Length Patterns
....................................................... 157
10.10
Intron
Organization and Evolution
.............................................. 158
10.11
Exercises
...................................................................................... 159
References
................................................................................................. 160
Index
................................................................................................................. 163
|
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author | Kangueane, Pandjassarame |
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author_sort | Kangueane, Pandjassarame |
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bvnumber | BV035556443 |
classification_rvk | WC 7700 WD 5100 |
classification_tum | BIO 110f |
ctrlnum | (OCoLC)634707459 (DE-599)DNB993294537 |
discipline | Biologie Informatik |
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id | DE-604.BV035556443 |
illustrated | Illustrated |
indexdate | 2024-07-09T21:40:21Z |
institution | BVB |
isbn | 9781441905185 |
language | English |
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physical | XXV, 166 S. Ill., graph. Darst. |
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publishDateSearch | 2009 |
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publisher | Springer |
record_format | marc |
spelling | Kangueane, Pandjassarame Verfasser aut Bioinformation discovery data to knowledge in biology Pandjassarame Kangueane New York, NY [u.a.] Springer 2009 XXV, 166 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wissensextraktion (DE-588)4546354-2 gnd rswk-swf Molekülstruktur (DE-588)4170383-2 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Data Science (DE-588)1140936166 gnd rswk-swf Biologie (DE-588)4006851-1 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Proteine (DE-588)4076388-2 s Molekülstruktur (DE-588)4170383-2 s Molekulare Bioinformatik (DE-588)4531334-9 s DE-604 Bioinformatik (DE-588)4611085-9 s Biologie (DE-588)4006851-1 s Data Science (DE-588)1140936166 s Wissensextraktion (DE-588)4546354-2 s 1\p DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017612248&sequence=000002&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 | Kangueane, Pandjassarame Bioinformation discovery data to knowledge in biology Wissensextraktion (DE-588)4546354-2 gnd Molekülstruktur (DE-588)4170383-2 gnd Proteine (DE-588)4076388-2 gnd Data Science (DE-588)1140936166 gnd Biologie (DE-588)4006851-1 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd Bioinformatik (DE-588)4611085-9 gnd |
subject_GND | (DE-588)4546354-2 (DE-588)4170383-2 (DE-588)4076388-2 (DE-588)1140936166 (DE-588)4006851-1 (DE-588)4531334-9 (DE-588)4611085-9 |
title | Bioinformation discovery data to knowledge in biology |
title_auth | Bioinformation discovery data to knowledge in biology |
title_exact_search | Bioinformation discovery data to knowledge in biology |
title_full | Bioinformation discovery data to knowledge in biology Pandjassarame Kangueane |
title_fullStr | Bioinformation discovery data to knowledge in biology Pandjassarame Kangueane |
title_full_unstemmed | Bioinformation discovery data to knowledge in biology Pandjassarame Kangueane |
title_short | Bioinformation discovery |
title_sort | bioinformation discovery data to knowledge in biology |
title_sub | data to knowledge in biology |
topic | Wissensextraktion (DE-588)4546354-2 gnd Molekülstruktur (DE-588)4170383-2 gnd Proteine (DE-588)4076388-2 gnd Data Science (DE-588)1140936166 gnd Biologie (DE-588)4006851-1 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd Bioinformatik (DE-588)4611085-9 gnd |
topic_facet | Wissensextraktion Molekülstruktur Proteine Data Science Biologie Molekulare Bioinformatik Bioinformatik |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017612248&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT kangueanepandjassarame bioinformationdiscoverydatatoknowledgeinbiology |