Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model:
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| Main Author: | |
|---|---|
| Format: | Microfilm Book |
| Language: | English |
| Published: |
[2004]
|
| Edition: | [Mikrofiche-Ausg.] |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Bonn, Univ., Diss., 2004 |
| Physical Description: | 118 S. graph. Darst. |
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| 245 | 1 | 0 | |a Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |c von Peter Wegner |
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| 264 | 1 | |c [2004] | |
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Record in the Search Index
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| adam_text |
CONTENTS
1
INTRODUCTION
9
1.1
MOTIVATION
.
9
1.2
BIOLOGICAL
BACKGROUND
.
11
1.3
OUTLINE
OF
THE
THESIS
.
18
2
THE
HYDROPHOBIC-HYDROPHILIC
MODEL
21
2.1
FORMAL
DEFINITIONS
.
23
3
COMPUTATIONAL
COMPLEXITY
THEORY
27
3.1
DECISION
PROBLEMS
.
27
3.2
CLASSIFICATION
OF
HARD
PROBLEMS
.
30
4
HARDNESS
FOR
COMPUTING
EXACT
SOLUTIONS
33
4.1
NP-HARDNESS
RESULTS
.
33
4.2
IMPORTANT
SPECIAL
CASE
THAT
IS
EASY
TO
SOLVE
.
38
4.3
COMPUTING
EXACT
SOLUTIONS
.
42
5
HARDNESS
RESULTS
ON
APPROXIMATE
SOLUTIONS
45
5.1
INTRODUCTION
TO
APPROXIMATION
ALGORITHMS
.
45
5.2
APPROXIMATION
HARDNESS
.
47
6
CONTENTS
6
APPROXIMATIVE
FOLDING
ALGORITHMS
51
6.1
UPPER
BOUNDS
ON
OPTIMAL
SOLUTIONS
.
52
6.2
HART
AND
ISTRAIL
'
S
4-APPROXIMATION
ALGORITHM
A
.
53
6.3
CHOOSING
A
MORE
APPROPRIATE
FOLDING
POINT
.
55
6.4
IMPROVING
THE
APPROXIMATION
RATIO
.
56
6.4.1
ASYMPTOTIC
4-APPROXIMATION
ALGORITHM
B
.
59
6.4.2
ASYMPTOTIC
3-APPROXIMATION
ALGORITHM
C
.
62
6.5
APPROXIMATION
BOUNDS
.
63
6.5.1
ANALYSIS
OF
ALGORITHM
A
.
64
6.5.2
FIRST
MODIFICATION:
BENDING
THE
TIPS
OF
THE
STEMS
.
65
6.5.3
SECOND
MODIFICATION:
SHIFTING
OF
THE
FOLDING
POINT
.
65
6.5.4
ANALYSIS
OF
ALGORITHM
B
.
65
6.5.5
ANALYSIS
OF
ALGORITHM
C
.
66
7
PREDICTIVE
PROTEIN
FOLDING
IN
HIGHER
DIMENSIONS
71
7.1
HP
FOLDING
PREDICTION
IN
THE
3D
SQUARE
LATTICE
.
72
7.1.1
UPPER
BOUND
FOR
OPTIMAL
SOLUTIONS
.
72
7.1.2
ASYMPTOTIC
4-APPROXIMATION
ALGORITHM
T
.
73
7.1.3
CONSTRUCTING
A
STAIRWAY:
8/3
APPROXIMATION
ALGORITHM
.
.
78
7.1.4
COMPACTING
THE
HYDROPHOBIC
CORE:
ALGORITHM
EK
.
80
7.1.5
TRADEOFF
BETWEEN
COMPACTNESS
AND
SCORE:
ALGORITHM
QK
.
81
7.2
HP-FOLD
IN
THE
D-DIMENSIONAL
SQUARE
LATTICE:
ALGORITHM
HK
.
85
7.2.1
FOLDING
IN
THE
TRIANGULAR
LATTICE:
ALGORITHM
I
D
.
92
8
EXPONENTIAL
SPEEDUP:
EFFICIENT
PARALLELIZATION
95
CONTENTS
7
8.1
PARALLEL
COMPUTATION
MODELS
.
95
8.2
THE
PRAM
MODEL
.
96
8.3
PARALLEL
FOLDING
ALGORITHMS
.
97
8.3.1
AN
OPTIMAL
PARALLEL
IMPLEMENTATION
OF
ALGORITHM
B
.
98
8.3.2
AN
EFFICIENT
PARALLEL
IMPLEMENTATION
OF
ALGORITHM
C
.
100
9
EMPIRICAL
RESULTS
103
10
CONCLUSION
AND
FURTHER
RESEARCH
105
10.1
FURTHER
RESEARCH
.
107 |
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| edition | [Mikrofiche-Ausg.] |
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| indexdate | 2024-11-05T13:04:53Z |
| institution | BVB |
| language | English |
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| spelling | Wegner, Peter 1970- Verfasser (DE-588)129703443 aut Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model von Peter Wegner [Mikrofiche-Ausg.] [2004] 118 S. graph. Darst. txt rdacontent h rdamedia he rdacarrier Bonn, Univ., Diss., 2004 Mikroform-Ausgabe Ketsch/ Rhein Mikroform 2004 2 Mikrofiches : 24x Approximationsalgorithmus (DE-588)4500954-5 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Lipophiles Verhalten (DE-588)4279756-1 gnd rswk-swf Hydrophiles Verhalten (DE-588)4285105-1 gnd rswk-swf Aminosäurensequenz (DE-588)4192666-3 gnd rswk-swf Berechnungskomplexität (DE-588)4134751-1 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Proteinfaltung (DE-588)4324567-5 s Berechnungskomplexität (DE-588)4134751-1 s Approximationsalgorithmus (DE-588)4500954-5 s Aminosäurensequenz (DE-588)4192666-3 s Lipophiles Verhalten (DE-588)4279756-1 s Hydrophiles Verhalten (DE-588)4285105-1 s DE-604 Reproduktion von Wegner, Peter, 1970- Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model [2004] DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014167867&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Wegner, Peter 1970- Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model Approximationsalgorithmus (DE-588)4500954-5 gnd Proteinfaltung (DE-588)4324567-5 gnd Lipophiles Verhalten (DE-588)4279756-1 gnd Hydrophiles Verhalten (DE-588)4285105-1 gnd Aminosäurensequenz (DE-588)4192666-3 gnd Berechnungskomplexität (DE-588)4134751-1 gnd |
| subject_GND | (DE-588)4500954-5 (DE-588)4324567-5 (DE-588)4279756-1 (DE-588)4285105-1 (DE-588)4192666-3 (DE-588)4134751-1 (DE-588)4113937-9 |
| title | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| title_auth | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| title_exact_search | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| title_exact_search_txtP | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| title_full | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model von Peter Wegner |
| title_fullStr | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model von Peter Wegner |
| title_full_unstemmed | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model von Peter Wegner |
| title_short | Efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| title_sort | efficient approximation algorithms for protein folding in the hydrophobic hydrophilic model |
| topic | Approximationsalgorithmus (DE-588)4500954-5 gnd Proteinfaltung (DE-588)4324567-5 gnd Lipophiles Verhalten (DE-588)4279756-1 gnd Hydrophiles Verhalten (DE-588)4285105-1 gnd Aminosäurensequenz (DE-588)4192666-3 gnd Berechnungskomplexität (DE-588)4134751-1 gnd |
| topic_facet | Approximationsalgorithmus Proteinfaltung Lipophiles Verhalten Hydrophiles Verhalten Aminosäurensequenz Berechnungskomplexität Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014167867&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT wegnerpeter efficientapproximationalgorithmsforproteinfoldinginthehydrophobichydrophilicmodel |