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Биологические базы данных #1
- 1. Биоинформатика. Базы данных Порозов Юрий. porozov@sns.it porozov@ifc.cnr.it
- 5. Bioinformatics - A New Discipline Взято из : D. Gilberts & C. Tan, 2002 http://www.brc.dcs.gla.ac.uk/~drg/courses/bioinformatics_city/slides/slides1/sld018.htm Large scale analysis and interpretation of genomics data. Computing Math& Stats Life sciences Physical sciences
- 7. Goal: Enable the discovery of new biological insights and create a global perspective for life sciences. Data produced by bio-labs and stored in database. Better biological and medical understanding. Bio-Informatics Algorithms and Tools Это вычислительные методы для глобального понимания биологических данных . Что такое биоинформатика ?
- 8. Биоинформатика Structural Genomics Pharmaco-Genomics Functional Genomics Proteomics Genomics Bioinformatics
- 12. ДНК
- 13. ДНК O O=P-O O Фосфатная группа N Азотистое основание (A, G, C, or T) CH2 O C 1 C 4 C 3 C 2 5 Сахар (дезоксирибоза)
- 14. ДНК ДНК состоит из двух цепей нуклеотидов, соединённых попарно : ADENINE – THYMINE CYTOSINE - GUANINE Правило комплементарности
- 15. Двойная спираль P P P O O O 1 2 3 4 5 5 3 3 5 P P P O O O 1 2 3 4 5 5 3 5 3 G C T A
- 17. Биополимеры - ДНК J. Watson и F. Crick. Фото из архива Photo Researchers inc.
- 18. ДНК, дальнейшая упаковка.
- 19. ДНК Функции ДНК — наследственность и изменчивость.
- 20. Репликация ДНК Репликация ДНК
- 25. GenBank. Запись sequence
- 26. GenBank. Запись mRNA
- 27. Сплайсинг и восстановление последовательности mRNA mRNA seq=(AF018429.1:282-561)+(AF018429.1:1034-1172)+(AF018430.1:560-651)+(AF018430.1:1-45)+………
- 28. GenBank. Запись genomic DNA
- 33. HELIX 1 1 GLU A 5 THR A 9 5 5 HELIX 2 2 ALA A 37 YOF A 39 5 3 HELIX 3 3 PRO A 56 VAL A 61 5 6 HELIX 4 4 VAL A 68 SER A 72 5 5 HELIX 5 5 PRO A 75 HIS A 81 5 7 HELIX 6 6 ASP A 82 ALA A 87 1 6 SHEET 1 A12 VAL A 12 VAL A 22 0 SHEET 2 A12 HIS A 25 ASP A 36 -1 O GLY A 31 N VAL A 16 SHEET 3 A12 LYS A 41 CYS A 48 -1 O THR A 43 N GLU A 34 SHEET 4 A12 HIS A 217 ALA A 227 -1 O LEU A 220 N LEU A 44 SHEET 5 A12 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 A12 ASN A 149 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 A12 GLY A 160 ASN A 170 -1 O GLY A 160 N ASP A 155 SHEET 8 A12 VAL A 176 PRO A 187 -1 O GLN A 177 N HIS A 169 SHEET 9 A12 YOF A 92 PHE A 100 -1 N GLU A 95 O GLN A 184 SHEET 10 A12 ASN A 105 GLU A 115 -1 O YOF A 106 N ILE A 98 SHEET 11 A12 THR A 118 ILE A 128 -1 O LYS A 126 N LYS A 107 SHEET 12 A12 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 CISPEP 1 MET A 88 PRO A 89 0 0.50 CRYST1 51.003 62.430 70.931 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014098 0.00000 ATOM 1 N SER A 2 28.277 8.150 50.951 1.00 57.00 N ATOM 2 CA SER A 2 27.454 9.223 51.584 1.00 55.40 C ATOM 3 C SER A 2 25.972 8.992 51.295 1.00 55.44 C ATOM 4 O SER A 2 25.576 7.932 50.799 1.00 54.37 O ATOM 5 CB SER A 2 27.883 10.601 51.046 1.00 70.82 C ATOM 6 OG SER A 2 27.150 11.676 51.622 1.00 71.45 O ATOM 7 N LYS A 3 25.157 9.993 51.619 1.00141.28 N ATOM 8 CA LYS A 3 23.716 9.932 51.398 1.00140.16 C -----------------------------------//---------------------------------------------------------------- ATOM 47 CA PHE A 8 26.551 11.090 41.294 1.00 19.27 C ATOM 48 C PHE A 8 27.751 10.357 40.676 1.00 21.43 C ATOM 49 O PHE A 8 28.562 10.924 39.938 1.00 21.44 O ATOM 50 CB PHE A 8 27.022 12.362 41.991 1.00 21.68 C ATOM 51 CG PHE A 8 25.909 13.297 42.288 1.00 17.60 C ATOM 52 CD1 PHE A 8 25.488 14.212 41.321 1.00 14.95 C ATOM 495 CA VAL A 68 23.860 22.610 40.452 1.00 14.12 C ATOM 496 C VAL A 68 25.259 22.196 40.854 1.00 13.41 C ATOM 1164 CA SER A 147 37.123 31.083 35.325 1.00 21.88 C ATOM 1819 CD1 ILE A 229 38.888 21.450 53.055 1.00 29.11 C ATOM 1820 OXT ILE A 229 43.220 19.637 50.148 1.00 25.25 O TER 1821 ILE A 229 HETATM 1822 O HOH 1 30.450 20.682 37.367 1.00 15.75 O HETATM 1823 O HOH 2 26.443 24.175 38.999 1.00 18.82 O ---------------------------------//------------------------------------------------ HETATM 1831 O HOH 10 29.132 18.648 45.101 1.00 13.77 O HETATM 1832 O HOH 11 24.076 46.248 42.794 1.00 22.62 O HETATM 1833 O HOH 12 31.870 32.426 52.146 1.00 36.77 O HETATM 1880 O HOH 59 37.243 14.571 53.463 1.00 31.12 O HETATM 1881 O HOH 60 40.360 20.483 56.144 1.00 32.74 O HETATM 1882 O HOH 61 13.483 49.374 33.179 1.00 30.77 O CONECT 267 268 CONECT 268 267 269 271 CONECT 819 820 CONECT 1594 1592 1596 1598 CONECT 1595 1593 1596 CONECT 1596 1594 1595 1597 CONECT 1597 1596 CONECT 1598 1594 MASTER 259 0 10 6 12 0 0 6 1881 1 140 18 END
- 40. Источники информации и базы данных в Интернете
- 45. NCBI ( National center for biotechnology information ) NCBI PubMed Books OMIM Nucleotides Proteins Genomes Taxonomy Structure Domains Exp’ profiles
- 55. Поиск белка в Swiss-Prot ( по названию)
- 56. Advances search
- 57. Результаты
- 59. Сохранить в FASTA формате
- 60. Стандартная запись Swiss-Prot
- 61. Стандартные поля : entry, name, origin Название записи, уникальный идентификатор ( ID) , предыдущие идентификаторы соответствующей записи, даты первой и последней модификаций, распространенное название белка и его синонимы ( EC номер для ферментов), название гена, организм и его таксономия, уровень подтверждения
- 63. Taxonomy Browser
- 64. Ссылки на статьи, использованные для аннотации
- 65. Комментарии
- 66. Продолжение
- 68. Cross-References
- 70. 3 D-Structure (список структур)
- 71. Reactome
- 72. GO terms Определение термина, синонимы, родительские ( Hierarchy) и дочерние термины , ключевые слова, дата последней модификации
- 73. Cross-References , Keywords
- 74. KEGG Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg/
- 75. KEGG ( pathway viewer)
- 76. DrugBank
- 77. Keywords
- 79. Feature Table
- 80. Координаты в Feature table
- 81. Feature table, продолжение
- 82. Feature Table, продолжение Только экспериментальные
- 83. Feature Table viewer (Sequence Element viewer)
- 84. Feature aligner Можно построить множественное выравнивание подмножества этих элементов ( ClustalW) или скопировать их в FASTA формате
- 85. Sequence
- 87. FASTA format Программа FASTA (1988, WR Pearson & DJ Lipman): >(the definition line) _уникальный_ ID + короткое описание ПОСЛЕДОВАТЕЛЬНОСТЬ БЕЛКА (ИЛИ ДНК) В ОДНОБУКВЕННОМ КОДЕ RAW format – без definition line
- 88. NiceProt view
- 89. Базы данных На 22.02.2011 PDB Exp.Method Proteins Nucleic Acids Protein/NA Complexes Other Total
- 90. Базы данных OCA
- 97. NCBI ( National center for biotechnology information ) NCBI PubMed Books OMIM Nucleotides Proteins Genomes Taxonomy Structure Domains Exp’ profiles
- 115. ProtParam - предсказание физико-химических параметров белка
- 117. Compute pI/Mw
- 118. PeptideMass
- 119. PeptideMass - output
- 120. PeptideCutter
- 121. PeptideCutter - output
- 122. PeptideCutter - output
- 124. Предсказание трансмембранных сегментов : ProtScale 56 аминокислотных шкал (с литературными ссылками), скользящее окно - > выбор ширины окна
- 125. ProtScale - output
- 126. Более сложное предсказание трансмембранных сегментов : TMHMM Transmembrane beta barrel prediction: PROFtmb (http://rostlab.org/services/proftmb ) ; PRED-TMBB ( http://biophysics.biol.uoa.gr/PRED-TMBB/ ) ; TBBPred ( http://www.imtech.res.in/raghava/tbbpred )
- 127. TMHMM - результаты TMHMM предсказывает сегменты, а также топологию межсегментных участков Наход ит только 7! TMs
- 131. InterPro Database .
- 134. Поиск доменов : InterProScan
- 135. InterProScan - результаты
- 136. Table View
- 137. CD server Input - Accession number , gi или последовательность в FASTA формате
- 138. CD server – output Красный – SMART, синий – Pfam, зеленый – COGs Рваные концы указывают на неполные домены!!!! Курсор в графической части – краткое описание функции домена
- 139. CDART – поиск белков с аналогичной доменной структурой
- 140. Pfscan Как правило, работает несколько минут
- 144. Superfamily : Probable common evolutionary origin Белки, имеющие низкую идентичность последовательностей, но чьи структурные и функциональные особенности позволяют предположить наличие общего предка, могут быть объединены в суперсемейства . Например, актин , the ATPase domain белков теплового шока и гексакиназы образуют суперсемейство Fold : Major structural similarity Общий фолд – одинаковая организация вторичной струкруры, с похожим пространственным расположением и с похожими соединениями . Белки с одинаковым фолдом зачастую имеют концевые элементы вторичной структуры , изгибы и повороты различных разметов и конформаций (до половины всей структуры) . Белки, объединённые одним фолдом, могут не иметь общего предка (химия, физика упаковка и топология) SCOP
- 145. SCOP Family : Clear evolutionarily relationship Белки, сгруппированные в семейство, тесно связаны эволюционно. Это значит, что парное выравнивание показывает 30 % и выше . Иногда похожие функция и структура показывают наличие общего предка и при отсутствии высокой идентичности последовательностей ; например , многие глобины образуют семейство, хотя некоторые из них имеют идентичность 1 D ~ 15%.
- 146. Archetype Structures of Domains
- 147. Поиск по SCOP
- 148. SCOP
- 155. DALI anti parallel barrel meander More information about DALI Touring protein fold space with Dali/FSSP: Liisa Holm and Chris Sander Comparing protein structures in 3D
- 158. DALI • Базируется на выравненных 2D матрицах внутримолекулярных дистанций • Считает лучший subset соответствующих аминокислот в двух белках – максимальная похожесть 2D матриц дистанций • Поиск по всем возможным выравниваниям остатков – Monte-Carlo и branch-and-bound algorithms An intra-molecular distance plot for myoglobin
- 161. PClass Database Инструмент для классификации, базирующийся на иерархии 600 белков-представителей из PDB. Структурное выравнивание 600 структур было выполнено при помощи алгоритма 3dSearch.
- 169. WHAT_CHECK Criteria Peptide-Pl: RMS distance of the backbone oxygen from the oxygen in similar backbone conformations found in the database, distances in the range [3..1] are mapped to [0..9] Rotamer: Probability that the sidechain rotamer (chi-1 only) is correct, probabilities in the range [0.1 .. 0.9] are mapped to [0..9] Chi-1/Chi-2: Z-score for the sidechain chi-1/chi-2 combination, Z-scores in the range probabilities in the range [-4..+4] are mapped to [0..9] Bumps: Sum of bumps per residue, distances in the range [0.1 .. 0] are mapped to [0..9]. Packing 1: First packing quality Z-score, Z-scores in the range [-5..+5] are mapped to [0..9]. Packing 2: Second packing quality Z-score, Z-scores in the range [-3..+3] are mapped to [0..9]. In/Out: Absolute inside/outside distribution Z-score per residue, Z-scores in the range [4..2] are mapped to [0..9]. H-Bonds: 9 minus number of unsatisfied hydrogen bonds, 2 is subtracted for buried backbone nitrogen, 5 for buried sidechain. Flips: Indicates flipped Asn/Gln/His sidechain, 9=OK, 0=needs flipping.
- 170. WHAT_CHECK Criteria Access: Relative side chain accessibility, 0=buried, 9=exposed. Quality: Several quality estimators from the PDBREPORTs.0=is oh no, 9=perfect. B-Factors: Crystallographic B-factors, the range [10..60] is mapped to [9..0] Bonds: Absolute Z-score of the largest bond deviation per residue, absolute Z-Scores in the range [5..2] are mapped to [0..9]. Angles: Absolute Z-score of the largest angle deviation per residue, absolute Z-Scores in the range [5..2] are mapped to [0..9]. Torsions: Average Z-score of the torsion angles per residue, Z-Scores in the range [-3..+3] are mapped to [0..9]. Phi/Psi: Ramachandran Z-score per residue, Z-Scores in the range [-4..+4] are mapped to [0..9]. Planarity: Z-score for the planarity of the residue sidechain, Z-Scores in the range [6..2] are mapped to [0..9]. Chirality: Average absolute Z-score of the chirality deviations per residue, average absolute Z-Scores in the range [4..2] are mapped to [0..9]. Backbone: Number of similar backbone conformations found in the database, numbers in the range [0..10] are mapped to [0..9]
- 172. Procheck. Отчёты
- 178. Способы визуализации
- 179. Для чего визуализация? ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS
- 180. An Introduction to Protein Architecture By A. M. Lesk
- 182. RasMol
- 183. RasTop
- 186. Protein Explorer
- 187. Protein Explorer
- 188. ExPASy
- 191. RasMol – Главное меню
- 192. RasMol - Дисплей
- 193. RasMol - Цвет
- 194. RasMol – Опции Сечение
- 195. RasMol – Опции Атомы H
- 196. RasMol – Опции Зеркальная поверхность
- 197. RasMol – Опции Тени
- 198. RasMol – Опции Стерео
- 199. RasMol – Опции Метки
- 200. RasMol - Экспорт
- 201. RasMol - Help
- 202. RasMol Manual RasMol 2.6 Manual http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual RasMol 2.7 Manual http://www.rasmol.org/
- 204. Swiss-PDBViewer Домашняя страница : http://ca.expasy.org/spdbv/ Руководство пользователя http://ca.expasy.org/spdbv/text/tutorial.htm.
- 205. Swiss-PDBViewer
Notas del editor
- Устно
- The classes are based on Levitt, M. & Chothia, C 1.Family: Clear evolutionarily relationship. Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are 30% and greater. However, in some cases similar functions and structures provide definitive evidence of common descent in the absense of high sequence identity; for example, many globins form a family though some members have sequence identities of only 15%. 2.Superfamily: Probable common evolutionary origin. Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed together in superfamilies. For example, actin, the ATPase domain of the heat shock protein, and hexakinase together form a superfamily. 3.Fold: Major structural similarity. Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation. In some cases, these differing peripheral regions may comprise half the structure. Proteins placed together in the same fold category may not have a common evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies.
- Устное.
- Domain – A poly peptide chain or fragment (100-200 aa) which fold into stable tertiary structure.
- Pfam is a database of two parts, the first is the curated part of Pfam containing over 3,700 protein families. To give Pfam a more comprehensive coverage of known proteins we automatically generate a supplement called Pfam-B. This contains a large number of small families taken from the PRODOM database that do not overlap with Pfam-A. Although of lower quality Pfam-B families can be useful when no Pfam-A families are found.
- HOMSTRAD (HOMologous STRucture Alignment Database) provides aligned three-dimensional structures of homologous proteins. The word homology is only used to mean having a common evolutionary origin, but we practically define homologous families as a group of proteins with sufficiently high sequence identities. We combine the classifications proposed by various databases including SCOP , Pfam , PROSITE and SMART and the results from sequence similarity searches by PSI-BLAST and FUGUE and make our own decisions to define the families. Our focus is to collect reasonable sets of protein sequences, where functionally and structurally important residues can be correctly aligned and highlighted. For example, even if a highly conserved local sequence motif is shared by a diverse group of proteins, it is sometimes difficult to align all the sequences on the basis of their structures. In such a case, we split the group into several smaller ones and call them families. On the other hand, some families defined in HOMSTRAD include protein pairs with fairly low overall sequence similarity but they still present convincing structure-based alignments. The central element of HOMSTRAD is a collection of carefully examined structure-based alignments organised at the level of homologous families. This requires substantial manual editing and is complementary to fully automated structure comparisons such as FSSP. One unique feature of HOMSTRAD is to display the alignments in a specially devised annotated form to help understand the conservation of various structural features. The analysis and annotation is carried out by the program JOY. See the software section for further details of this format. The combination of HOMSTRAD and JOY proved to be particularly useful in achieving accurate alignments for comparative modelling (Burk et al., 1999). This facility, again, contrasts some other database resources such as SCOP (Murzin et al., 1995) and CATH (Orengo et al., 1997), which provide a hierarchical classification of protein structures.
- Устное объяснение
- Устное объяснение
- toms with non-zero accessible surface area could not be handled, because they are not completely surrounded by other atoms, and their Voronoi volume can therefore not be defined. A negative Z-score means that the atom has a smaller than average volume, whereas a positive score indicates that an atom has a larger than average volume.
- Цитохром Rhodopseudomonas viridis. Note the symmetry of LM = 60% identity
- 1wqa, 1tx4, 1grn, 1tad and 1gfi. -> only 1tx4, 1grn, 1tad Note that some amino acids may appear in yellow once a molecule has been loaded. It signifies that their sidechain has been reconstructed during the loading process because some atoms were lacking. When all sidechain atoms are lacking, a rotamer library is searched until the rotamer that generate a maximum of H-bonds and a minimum of steric hindrances is found. If only some sidechain atoms are lacking, the rotamer that gives the lowest RMS when fitted to the partial sidechain is taken. In any case, you may try to find a better sidechain manually with the mutation tool. If you want to act on a complete column , simply hold down the shift key while clicking in a column Note: if a little earth icon is shown below the first tool, the rotation takes place in absolute coordinates. Otherwise (little protein icon) molecules are rotated around their centrotid. Hence the first option allows you to rotate the molecule around any atom, providing that this atom has previously been centered (translated to the (0,0,0) coordinate). Note: if "caps lock" is down, you can measure several distances or angles successively. To exit the "repeated" measurement mode, you can either depress "caps lock" or hit "esc".