Protein folding in silico: protein folding versus protein structure prediction
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Oxford [u.a.]
Woodhead Publ.
2012
|
| Series: | Woodhead publishing series in biomedicine
22 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXXI, 208 S. Ill., graph. Darst. |
| ISBN: | 9781907568176 |
Staff View
MARC
| LEADER | 00000nam a2200000 cb4500 | ||
|---|---|---|---|
| 001 | BV040675582 | ||
| 003 | DE-604 | ||
| 005 | 20130221 | ||
| 007 | t | ||
| 008 | 130116s2012 ad|| |||| 00||| eng d | ||
| 020 | |a 9781907568176 |9 978-1-907568-17-6 | ||
| 035 | |a (OCoLC)824710965 | ||
| 035 | |a (DE-599)BVBBV040675582 | ||
| 040 | |a DE-604 |b ger |e rakwb | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-355 | ||
| 082 | 0 | |a 572.633 | |
| 084 | |a WC 7700 |0 (DE-625)148144: |2 rvk | ||
| 084 | |a WD 5100 |0 (DE-625)148194: |2 rvk | ||
| 245 | 1 | 0 | |a Protein folding in silico |b protein folding versus protein structure prediction |c ed. by Irena Roterman-Konieczna |
| 264 | 1 | |a Oxford [u.a.] |b Woodhead Publ. |c 2012 | |
| 300 | |a XXXI, 208 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Woodhead publishing series in biomedicine |v 22 | |
| 650 | 0 | 7 | |a Proteinfaltung |0 (DE-588)4324567-5 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a In silico-Methode |0 (DE-588)4816890-7 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4143413-4 |a Aufsatzsammlung |2 gnd-content | |
| 689 | 0 | 0 | |a Proteinfaltung |0 (DE-588)4324567-5 |D s |
| 689 | 0 | 1 | |a In silico-Methode |0 (DE-588)4816890-7 |D s |
| 689 | 0 | |C b |5 DE-604 | |
| 700 | 1 | |a Roterman-Konieczna, Irena |e Sonstige |4 oth | |
| 830 | 0 | |a Woodhead publishing series in biomedicine |v 22 |w (DE-604)BV040675553 |9 22 | |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025502069&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-025502069 | ||
Record in the Search Index
| _version_ | 1804149805263355904 |
|---|---|
| adam_text | Contents
List of figures
xv
List of tables
xix
About the editor
xxi
List of contributors
xxv
Introduction
xxvii
/.
Roterman-Konieczna
1
The early-stage intermediate
1
W. Jurkowski, Z.
Baster, D.
Dutak, and
I. Roterman-Konieczna
1.1
Geometric model
2
1.2
Structural alphabet
5
1.3
Contingency table
11
1.4
In search of structural similarities
17
1.5
References
18
1.6
Suggested reading
20
2
The late-stage intermediate
21
M. Banach,
L
Konieczny,
and I. Roterman-Konieczna
2.1
The fuzzy oil drop model
22
2.2
Quantitative description of the
hydrophobic core
25
I v
2.3
Protein characteristics with respect to the
hydrophobic core
29
2.4
Simulation of late-stage folding
30
xi
Published by Woodhead Publishing Limited,
2012
Protein
folding in silico
2.5
References
32
2.6
Suggested reading
33
Structural information involved in the interpretation
of the stepwise protein folding process
39
R
Alejster, W. Jurkowski, and I. Roterman-Konieczna
3.1
Balancing the quantity of information in the
amino
acid sequence and the early-stage
intermediate
40
3.2
Zones on the Ramachandran map
43
3.3
References
-...ч,/
< 50.
3.4
Suggested reading
51.
The divergence entropy characterizing the
.
internal force field in proteins
55
M. Banach, D.
Marchewka,
M.
Piwowar,
and
I. Roterman-Konieczna
4.1
Internal force field for nonbonding interactions
56
4.2
The impact of ligands
59
4.3
Structures of homodimers
-
protein-protein
interaction
61
4.4
Protein containing a catalytic center
64
4.5
The role of exons
65
4.6
Conclusions
71
4.7
References
74
5
Ligand-binding-site recognition
79
M. Banach,
L
Konieczny,
and
1.
Roterman-Konieczna
5.1
General model
80
5.2
ROC curves
80
5.3
Summary
. .--
89
5.4
References
л „г
■■■,. ..
90
5.5
Suggested reading
92
xii
Published by Woodhead Publishing Limited,
2012
Contents
6
Use of the fuzzy oil drop model to identify the
complexation area in protein homodimers
95
M. Banach,
L
Konieczny,
and I. Roterman-Konieczna
6.1
General description
96
6.2
ROC curves
99
6.3
Conclusions
115
6.4
References
119
6.5
Suggested reading
121
7
Simulation of the polypeptide chain folding
process using the fuzzy oil drop model
123
L.
Konieczny
and I. Roterman-Konieczna
7.1
Simulation of the folding process in the
presence of an external hydrophobic
force field
124
7.2
Folding in the presence of a ligand
133
7.3
Influence of external factors on polypeptide
chain folding
135
7.4
References
137
7.5
Suggested reading
138
8
Misfolded proteins
141
M.
Król,
L.
Konieczny,
K. Stapor,
Z. Wiśniowski,
W. Ziajka, G. Szoniec, and
I.
Roterman-Konieczna
8.1
Introduction
141
8.2
In silico experiment
142
8.3
Conclusions
151
8.4
Appendix
1:
details of the molecular
dynamics simulation
154
8.5
Appendix
2:
details of the cluster analysis
156
8.6
References
159
8.7
Suggested reading
161
xiii
Published by Woodhead Publishing Limited,
2012
Protein
folding in silico
9
A short description of other selected
ab
¡nitío f
methods for protein structure prediction
> ■ ? * -
>165
I. Roterman-Konieczna
·■ - - -> -
9.1
Introduction
■■< 165
9.2
Simplifying the geometric model and the
w.
field function
; ·, 169
9.3
Lattice model
,> 172
9.4
ROSETTA
;:·
174
9.5
In search of a global minimum
-
force field >
,., ,, -
deformation
. ..,. _., ,.,,177
9.6
References
·...·
r^
182
9.7
Suggested reading
u
,.-, ■ 187
9.8
Selected servers oriented toward protein
structure prediction available on the Internet
187
10
Conclusion
191
L.
Konieczny
and I. Roterman-Konieczna
■ ■
10.1
Acknowledgements
201
10.2
References
201
10.3
Suggested reading J
202
Index
..... *
°7*
203
xiv
Published by Woodhead Publishing Limited,
2012
|
| any_adam_object | 1 |
| building | Verbundindex |
| bvnumber | BV040675582 |
| classification_rvk | WC 7700 WD 5100 |
| ctrlnum | (OCoLC)824710965 (DE-599)BVBBV040675582 |
| dewey-full | 572.633 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.633 |
| dewey-search | 572.633 |
| dewey-sort | 3572.633 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01648nam a2200397 cb4500</leader><controlfield tag="001">BV040675582</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20130221 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">130116s2012 ad|| |||| 00||| eng d</controlfield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9781907568176</subfield><subfield code="9">978-1-907568-17-6</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)824710965</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV040675582</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-355</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">572.633</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WC 7700</subfield><subfield code="0">(DE-625)148144:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WD 5100</subfield><subfield code="0">(DE-625)148194:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Protein folding in silico</subfield><subfield code="b">protein folding versus protein structure prediction</subfield><subfield code="c">ed. by Irena Roterman-Konieczna</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Oxford [u.a.]</subfield><subfield code="b">Woodhead Publ.</subfield><subfield code="c">2012</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">XXXI, 208 S.</subfield><subfield code="b">Ill., graph. Darst.</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="490" ind1="1" ind2=" "><subfield code="a">Woodhead publishing series in biomedicine</subfield><subfield code="v">22</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Proteinfaltung</subfield><subfield code="0">(DE-588)4324567-5</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">In silico-Methode</subfield><subfield code="0">(DE-588)4816890-7</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4143413-4</subfield><subfield code="a">Aufsatzsammlung</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Proteinfaltung</subfield><subfield code="0">(DE-588)4324567-5</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="1"><subfield code="a">In silico-Methode</subfield><subfield code="0">(DE-588)4816890-7</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="C">b</subfield><subfield code="5">DE-604</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Roterman-Konieczna, Irena</subfield><subfield code="e">Sonstige</subfield><subfield code="4">oth</subfield></datafield><datafield tag="830" ind1=" " ind2="0"><subfield code="a">Woodhead publishing series in biomedicine</subfield><subfield code="v">22</subfield><subfield code="w">(DE-604)BV040675553</subfield><subfield code="9">22</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">Digitalisierung UB Regensburg</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=025502069&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-025502069</subfield></datafield></record></collection> |
| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV040675582 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:28:52Z |
| institution | BVB |
| isbn | 9781907568176 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-025502069 |
| oclc_num | 824710965 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | XXXI, 208 S. Ill., graph. Darst. |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Woodhead Publ. |
| record_format | marc |
| series | Woodhead publishing series in biomedicine |
| series2 | Woodhead publishing series in biomedicine |
| spelling | Protein folding in silico protein folding versus protein structure prediction ed. by Irena Roterman-Konieczna Oxford [u.a.] Woodhead Publ. 2012 XXXI, 208 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Woodhead publishing series in biomedicine 22 Proteinfaltung (DE-588)4324567-5 gnd rswk-swf In silico-Methode (DE-588)4816890-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Proteinfaltung (DE-588)4324567-5 s In silico-Methode (DE-588)4816890-7 s b DE-604 Roterman-Konieczna, Irena Sonstige oth Woodhead publishing series in biomedicine 22 (DE-604)BV040675553 22 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025502069&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein folding in silico protein folding versus protein structure prediction Woodhead publishing series in biomedicine Proteinfaltung (DE-588)4324567-5 gnd In silico-Methode (DE-588)4816890-7 gnd |
| subject_GND | (DE-588)4324567-5 (DE-588)4816890-7 (DE-588)4143413-4 |
| title | Protein folding in silico protein folding versus protein structure prediction |
| title_auth | Protein folding in silico protein folding versus protein structure prediction |
| title_exact_search | Protein folding in silico protein folding versus protein structure prediction |
| title_full | Protein folding in silico protein folding versus protein structure prediction ed. by Irena Roterman-Konieczna |
| title_fullStr | Protein folding in silico protein folding versus protein structure prediction ed. by Irena Roterman-Konieczna |
| title_full_unstemmed | Protein folding in silico protein folding versus protein structure prediction ed. by Irena Roterman-Konieczna |
| title_short | Protein folding in silico |
| title_sort | protein folding in silico protein folding versus protein structure prediction |
| title_sub | protein folding versus protein structure prediction |
| topic | Proteinfaltung (DE-588)4324567-5 gnd In silico-Methode (DE-588)4816890-7 gnd |
| topic_facet | Proteinfaltung In silico-Methode Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025502069&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV040675553 |
| work_keys_str_mv | AT rotermankoniecznairena proteinfoldinginsilicoproteinfoldingversusproteinstructureprediction |