Protein structure prediction with combinatorial optimization and fold recognition: = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English German |
| Published: |
2000
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Heidelberg, Univ., Diss., 2000. - Zsfassung in dt. Sprache |
| Physical Description: | 159 S. graph. Darst. : 30 cm |
Staff View
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV013903503 | ||
| 003 | DE-604 | ||
| 005 | 20020405 | ||
| 007 | t | ||
| 008 | 010828s2000 gw d||| m||| 00||| eng d | ||
| 016 | 7 | |a 960999655 |2 DE-101 | |
| 035 | |a (OCoLC)48729080 | ||
| 035 | |a (DE-599)BVBBV013903503 | ||
| 040 | |a DE-604 |b ger |e rakddb | ||
| 041 | 0 | |a eng |a ger | |
| 044 | |a gw |c DE | ||
| 049 | |a DE-29T |a DE-83 |a DE-188 | ||
| 100 | 1 | |a Bindewald, Eckart |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Protein structure prediction with combinatorial optimization and fold recognition |b = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |c by Eckart Bindewald |
| 246 | 1 | 1 | |a Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| 264 | 1 | |c 2000 | |
| 300 | |a 159 S. |b graph. Darst. : 30 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Heidelberg, Univ., Diss., 2000. - Zsfassung in dt. Sprache | ||
| 502 | |a Heidelberg, Univ., Diss., 2000 | ||
| 650 | 7 | |a Hochschulschrift |2 gtt | |
| 650 | 0 | 7 | |a Tertiärstruktur |0 (DE-588)4276602-3 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Proteine |0 (DE-588)4076388-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Molekulardesign |0 (DE-588)4265444-0 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 689 | 0 | 0 | |a Proteine |0 (DE-588)4076388-2 |D s |
| 689 | 0 | 1 | |a Tertiärstruktur |0 (DE-588)4276602-3 |D s |
| 689 | 0 | 2 | |a Molekulardesign |0 (DE-588)4265444-0 |D s |
| 689 | 0 | |5 DE-604 | |
| 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=009514560&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-009514560 | |
Record in the Search Index
| _version_ | 1812460881206837248 |
|---|---|
| adam_text |
CONTENTS
1 INTRODUCTION 1
1.1 WHY PROTEIN STRUCTURE PREDICTION IS IMPORTANT. 2
1.2 OUTLINE OF THIS THESIS. 2
1 BASICS 5
2 PROTEINS 7
2.1 AMINO ACIDS. 7
2.1.1 THE LOCAL STRUCTURE OF AMINO ACIDS. 9
2.2 SECONDARY STRUCTURE. 11
2.2.1 A-HELIX. 11
2.2.2 /3-SHEETS. 12
2.3 HOW PROTEINS FOLD. 12
2.3.1 THE "NEW VIEW" OF PROTEIN FOLDING. 13
2.4 DEFINITION OF ALIGNMENTS AND OF STRUCTURAL AND SEQUENCE SIM
ILARITY OF PROTEINS. 14
2.5 CLASSIFICATION OF PROTEIN STRUCTURES. 19
2.6 CLASSIFICATION OF THE FUNCTIONS OF PROTEINS. 21
3 PROTEIN STRUCTURE DETERMINATION / 23
3.1 HOW MANY PROTEIN STRUCTURES ARE KNOWN TODAY. 23
3.2 EXPERIMENTAL PROTEIN STRUCTURE DETERMINATION. 24
3.2.1 X-RAY CRYSTALLOGRAPHY. 24
BIBLIOGRAFISCHE INFORMATIONEN
HTTP://D-NB.INFO/960999655
CONTENTS
II
3.2.2 NMR TECHNIQUES. 24
3.3 SECONDARY STRUCTURE PREDICTION METHODS. 25
3.4 TERTIARY STRUCTURE PREDICTION METHODS. 27
3.4.1 COMPARATIVE MODELLING . 27
3.4.2 FOLD RECOGNITION. 32
3.4.3 AB INITIO METHODS. 34
4 GLOBAL OPTIMIZATION AND COMBINATORIAL OPTIMIZATION 37
4.1 GLOBAL OPTIMIZATION. 37
4.2 GLOBAL OPTIMIZATION AND THE NO FREE LUNCH THEOREM . 38
4.3 WHY THE POTENTIAL ENERGY IS SUFFICIENT FOR EXPLORING THE EN
ERGY LANDSCAPE. 39
4.4 MONTE CARLO AND SIMULATED ANNEALING. 41
4.5 MOLECULAR DYNAMICS. 41
4.6 GENETIC ALGORITHMS. 43
4.7 BRANCH & BOUND ALGORITHMS. 44
4.7.1 THE
ABB
ALGORITHM. 45
4.7.2 THE A* ALGORITHM. 46
4.8 OTHER OPTIMIZATION ALGORITHMS . 47
4.8.1 FLOOD ALGORITHM. 47
4.8.2 N-KEEP ALGORITHM. 48
5 PROTEIN ENERGY MODELS 49
5.1 COMPUTING PROTEIN STRUCTURE USING QUANTUM MECHANICAL MOD
ELS . 49
5.2 FORCE FIELDS. 51
5.3 KNOWLEDGE BASED POTENTIALS. 53
5.3.1 AMINO ACID BASED CONTACT POTENTIALS. 54
5.3.2 THE " STRUCTURE-DERIVED HYDROPHOBIC POTENTIAL" . 55
5.4 SUMMARY. 56
II AB INITIO PROTEIN STRUCTURE CALCULATIONS 59
6 THE BEST-PROFILE SEARCH ALGORITHM 61
6.1 BEST-FIRST SEARCH. 62
6.1.1 THE A* SEARCH ALGORITHM . 64
6.2 THE CANONICAL SEARCH ALGORITHM AND UNCOUPLED SPIN SYSTEMS 65
6.3 PROPERTIES OF THE CANONICAL SEARCH ALGORITHM. 67
6.4 THE BEST-PROFILE SEARCH ALGORITHM. 70
6.5 THE RANDOMIZED BEST-PROFILE SEARCH ALGORITHM. 72
6.6 SUMMARY. 72
7 DEVELOPMENT OF AN ORIENTATION DEPENDENT KNOWLEDGE BASED
POTENTIAL 75
CONTENTS
III
7.1 KNOWLEDGE BASED POTENTIALS. 75
7.1.1 THE PROBLEM OF SMALL DATA SETS. 77
7.2 THE USED DATA SET OF PROTEINS. 78
7.3 THE DATA ANALYSIS. 79
7.4 SUMMARY. 79
8 PUTTING THINGS TOGETHER: THE MOLEGO SYSTEM 81
8.1 REQUIREMENTS. 81
8.2 IMPLEMENTATION OF THE MOLEGO SYSTEM. 82
8.2.1 CLASS STRUCTURE OF THE BRANCH AND BOUND SYSTEM . . 83
8.2.2 CLASS STRUCTURE OF ENERGY MODELS. 85
8.2.3 DISCRETIZATION SCHEMES. 86
8.3 PROGRAM DESCRIPTION. 87
8.4 SUMMARY. 88
9 RESULTS 91
9.1 COMPARING THE BEST PROFILE SEARCH WITH OTHER OPTIMIZATION
ALGORITHMS.91
9.2 STRUCTURE PREDICTION ACCURACY WITH DIFFERENT SCORING FUNCTIONS 92
9.3 DISCUSSION. 93
9.4 SUMMARY. 96
HI FOLD RECOGNITION 99
10 MOTIVATION 101
11 RULES FOR THE RELATIONSHIP BETWEEN STRUCTURE AND FUNCTION
OF PROTEINS 105
11.1 THE RELATIONSHIP BETWEEN THE STRUCTURE AND FUNCTION OF PROTEINS 105
11.2 COMPLEXITIES OF THE PROTEIN STRUCTURE - FUNCTION RELATIONSHIP 106
11.3 ANALYSIS OF PROTEIN STRUCTURE - FUNCTION RELATIONSHIP BY OTHER
GROUPS.107
11.4 MY STRUCTURE-FUNCTION ANALYSIS USING THE FSSP STRUCTURE
DATABASE.108
11.5 DISCUSSION.ILL
11.6 SUMMARY.112
12 IMPLEMENTATION OF THE MANIFOLD FOLD RECOGNITION SYS
TEM / 113
12.1 THE IMPLEMENTED NEEDLEMAN-WUNSCH ALIGNMENT ALGORITHM . 114
12.2 THE IMPLEMENTED SIMILARITY CRITERIA.116
12.2.1 SEQUENCE SIMILARITY.116
12.2.2 SECONDARY STRUCTURE BLOCK SIMILARITY.117
IV CONTENTS
12.2.3 SIMULTANEOUS SECONDARY STRUCTURE AND ACCESSIBILITY
ALIGNMENT.117
12.2.4 RELATIVE LENGTH DIFFERENCE.118
12.2.5 FUNCTIONAL SIMILARITY.118
12.3 DECISION MAKING WITH MANY CRITERIA.119
12.4 THE FOLD LIBRARY.119
12.5 USAGE OF THE MANIFOLD SYSTEM.120
12.6 DISCUSSION AND SUMMARY.121
13 RESULTS OF THE MANIFOLD FOLD RECOGNITION SYSTEM 123
13.1 THE TEST DATA SET FOR EVALUATING THE PERFORMANCE OF THE FOLD
RECOGNITION SYSTEM.123
13.2 RESULTS.124
13.2.1 FOLD RECOGNITION THE CASP-4 TARGET T0100 : PECTIN
METHYLESTERASE.124
13.2.2 A TEST SET USED BY OTHER FOLD RECOGNITION PROGRAMS . 128
13.3 DISCUSSION.128
13.4 SUMMARY.130
14 SUMMARY 133
15 GLOSSARY 137
REFERENCES 141
A SETS OF PROTEINS WITH A SIMILAR FUNCTION FOR A GIVEN STRUC
TURE 153
B PROTEIN STRUCTURES USED FOR THE KNOWLEDGE BASED POTENTIAL 157 |
| any_adam_object | 1 |
| author | Bindewald, Eckart |
| author_facet | Bindewald, Eckart |
| author_role | aut |
| author_sort | Bindewald, Eckart |
| author_variant | e b eb |
| building | Verbundindex |
| bvnumber | BV013903503 |
| ctrlnum | (OCoLC)48729080 (DE-599)BVBBV013903503 |
| format | Thesis Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>00000nam a2200000 c 4500</leader><controlfield tag="001">BV013903503</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20020405</controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">010828s2000 gw d||| m||| 00||| eng d</controlfield><datafield tag="016" ind1="7" ind2=" "><subfield code="a">960999655</subfield><subfield code="2">DE-101</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)48729080</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV013903503</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakddb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield><subfield code="a">ger</subfield></datafield><datafield tag="044" ind1=" " ind2=" "><subfield code="a">gw</subfield><subfield code="c">DE</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-29T</subfield><subfield code="a">DE-83</subfield><subfield code="a">DE-188</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Bindewald, Eckart</subfield><subfield code="e">Verfasser</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Protein structure prediction with combinatorial optimization and fold recognition</subfield><subfield code="b">= Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung</subfield><subfield code="c">by Eckart Bindewald</subfield></datafield><datafield tag="246" ind1="1" ind2="1"><subfield code="a">Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2000</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">159 S.</subfield><subfield code="b">graph. Darst. : 30 cm</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">Heidelberg, Univ., Diss., 2000. - Zsfassung in dt. Sprache</subfield></datafield><datafield tag="502" ind1=" " ind2=" "><subfield code="a">Heidelberg, Univ., Diss., 2000</subfield></datafield><datafield tag="650" ind1=" " ind2="7"><subfield code="a">Hochschulschrift</subfield><subfield code="2">gtt</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Tertiärstruktur</subfield><subfield code="0">(DE-588)4276602-3</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Proteine</subfield><subfield code="0">(DE-588)4076388-2</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Molekulardesign</subfield><subfield code="0">(DE-588)4265444-0</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4113937-9</subfield><subfield code="a">Hochschulschrift</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Proteine</subfield><subfield code="0">(DE-588)4076388-2</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="1"><subfield code="a">Tertiärstruktur</subfield><subfield code="0">(DE-588)4276602-3</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="2"><subfield code="a">Molekulardesign</subfield><subfield code="0">(DE-588)4265444-0</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">DNB Datenaustausch</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009514560&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="943" ind1="1" ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-009514560</subfield></datafield></record></collection> |
| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV013903503 |
| illustrated | Illustrated |
| indexdate | 2024-10-09T18:09:49Z |
| institution | BVB |
| language | English German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-009514560 |
| oclc_num | 48729080 |
| open_access_boolean | |
| owner | DE-29T DE-83 DE-188 |
| owner_facet | DE-29T DE-83 DE-188 |
| physical | 159 S. graph. Darst. : 30 cm |
| publishDate | 2000 |
| publishDateSearch | 2000 |
| publishDateSort | 2000 |
| record_format | marc |
| spelling | Bindewald, Eckart Verfasser aut Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung by Eckart Bindewald Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung 2000 159 S. graph. Darst. : 30 cm txt rdacontent n rdamedia nc rdacarrier Heidelberg, Univ., Diss., 2000. - Zsfassung in dt. Sprache Heidelberg, Univ., Diss., 2000 Hochschulschrift gtt Tertiärstruktur (DE-588)4276602-3 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Molekulardesign (DE-588)4265444-0 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Proteine (DE-588)4076388-2 s Tertiärstruktur (DE-588)4276602-3 s Molekulardesign (DE-588)4265444-0 s DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009514560&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bindewald, Eckart Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung Hochschulschrift gtt Tertiärstruktur (DE-588)4276602-3 gnd Proteine (DE-588)4076388-2 gnd Molekulardesign (DE-588)4265444-0 gnd |
| subject_GND | (DE-588)4276602-3 (DE-588)4076388-2 (DE-588)4265444-0 (DE-588)4113937-9 |
| title | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| title_alt | Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| title_auth | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| title_exact_search | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| title_full | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung by Eckart Bindewald |
| title_fullStr | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung by Eckart Bindewald |
| title_full_unstemmed | Protein structure prediction with combinatorial optimization and fold recognition = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung by Eckart Bindewald |
| title_short | Protein structure prediction with combinatorial optimization and fold recognition |
| title_sort | protein structure prediction with combinatorial optimization and fold recognition proteinstrukturvorhersage mit kombinatorischer optimierung und faltungserkennung |
| title_sub | = Proteinstrukturvorhersage mit kombinatorischer Optimierung und Faltungserkennung |
| topic | Hochschulschrift gtt Tertiärstruktur (DE-588)4276602-3 gnd Proteine (DE-588)4076388-2 gnd Molekulardesign (DE-588)4265444-0 gnd |
| topic_facet | Hochschulschrift Tertiärstruktur Proteine Molekulardesign |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009514560&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT bindewaldeckart proteinstructurepredictionwithcombinatorialoptimizationandfoldrecognitionproteinstrukturvorhersagemitkombinatorischeroptimierungundfaltungserkennung AT bindewaldeckart proteinstrukturvorhersagemitkombinatorischeroptimierungundfaltungserkennung |