タンパク質関係のデータベースは、次の3種類がよく使われます
[1] タンパク質配列注釈＝UniProt
[2] タンパク質の立体構造＝PDB(Protein Data Bank)
[3] タンパク質の構造要素(ドメイン)＝InterPro
https://ja.wikipedia.org/wiki/Swiss-Prot
https://ja.wikipedia.org/wiki/%E8%9B%8B%E7%99%BD%E8%B3%AA%E6%A7%8B%E9%80%A0%E3%83%87%E3%83%BC%E3%82%BF%E3%83%90%E3%83%B3%E3%82%AF
https://ja.wikipedia.org/wiki/%E3%82%BF%E3%83%B3%E3%83%91%E3%82%AF%E8%B3%AA%E3%83%89%E3%83%A1%E3%82%A4%E3%83%B3
---[p.87]----------------------------------------------------
＜UniProtからの配列データ抽出＞
UniProtとは、欧EBIが提供する「タンパク質配列」の
機能注釈データベース
以下の4種類で構成されている。
名称 分類
1
UniProtKB
タンパク質配列の注釈DB
(1)Swiss-Prot:手動キュレーション済DB
(2)TrEMBL: 自動注釈DB
2
UniParc
配列アーカイブ（公共DBからの抽出セット）
3
UniRef 配列クラスタ
4
UniMes
環境メタゲノム配列
*biomartのライブラリが使えないので、p.89,8番～のUniProt.wsを使います
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for
> biocLite();
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
略
> biocLite("UniProt.ws")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
Installing package(s) ‘UniProt.ws’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/UniProt.ws_2.8.0.zip'
Content type 'application/zip' length 961852 bytes (939 KB)
downloaded 939 KB
package ‘UniProt.ws’ successfully unpacked and MD5 sums checked
> library(UniProt.ws)
要求されたパッケージ RSQLite をロード中です
要求されたパッケージ DBI をロード中です
要求されたパッケージ RCurl をロード中です
要求されたパッケージ bitops をロード中です
要求されたパッケージ BiocGenerics をロード中です
要求されたパッケージ parallel をロード中です
次のパッケージを付け加えます: ‘BiocGenerics’
略
------------------------------------------------
> availableUniprotSpecies("musculus")
taxon ID Species name
1 520121 Anthocoris musculus
2 208057 Anthoscopus musculus
3 238007 Apomys musculus
4 9771 Balaenoptera musculus
5 197864 Blepharisma musculus
6 10090 Mus musculus
7 35531 Mus musculus bactrianus
8 10091 Mus musculus castaneus
9 57486 Mus musculus molossinus
>
> availableUniprotSpecies("Homo")
taxon ID Species name
1 111945 Homoroselaps lacteus
2 63221 Homo sapiens neanderthalensis
3 9606 Homo sapiens
4 155619 Homobasidiomycetes
--------ヒトデータをセット------------------------------------
> UniProt.ws(9606)
"UniProt.ws" object:
An interface object for UniProt web services
Current Taxonomy ID:
9606
Current Species name:
Homo sapiens
To change Species see: help('availableUniprotSpecies')
> tmp <- UniProt.ws(9606) ヒトデータを選択
> species(tmp)
[1] "Homo sapiens"
> taxId(tmp)
[1] 9606
------利用可能なカラム--------------------------------------------------------
> columns(tmp)
[1] "UNIPROTKB" "UNIPARC"
[3] "UNIREF50" "UNIREF90"
[5] "UNIREF100" "EMBL/GENBANK/DDBJ"
[7] "EMBL/GENBANK/DDBJ_CDS" "PIR"
[9] "UNIGENE" "ENTREZ_GENE"
[11] "GI_NUMBER*" "REFSEQ_PROTEIN"
[13] "REFSEQ_NUCLEOTIDE" "PDB"
[15] "DISPROT" "HSSP"
[17] "DIP" "MINT"
[19] "ALLERGOME" "MEROPS"
[21] "PEROXIBASE" "PPTASEDB"
[23] "REBASE" "TCDB"
[25] "PHOSSITE" "DMDM"
[27] "AARHUS/GHENT-2DPAGE" "ECO2DBASE"
[29] "WORLD-2DPAGE" "DNASU"
[31] "ENSEMBL" "ENSEMBL_PROTEIN"
[33] "ENSEMBL_TRANSCRIPT" "ENSEMBL_GENOMES"
[35] "ENSEMBL_GENOMES PROTEIN" "ENSEMBL_GENOMES TRANSCRIPT"
[37] "KEGG" "PATRIC"
[39] "TIGR" "UCSC" [41] "VECTORBASE" "AGD" [43] "ARACHNOSERVER" "CGD"
[45] "CONOSERVER" "CYGD"
[47] "DICTYBASE" "ECHOBASE"
：
略
：
[97] "DOMAINS" "DOMAIN"
[99] "EC" "ID"
[101] "EXISTENCE" "FAMILIES" [103] "FEATURES" "GENES"
[105] "GO" "GO-ID"
[107] "INTERPRO" "INTERACTOR" [109] "KEYWORDS" "KEYWORD-ID" [111] "LAST-MODIFIED" "LENGTH" [113] "ORGANISM" "ORGANISM-ID" [115] "PATHWAY" "REVIEWED" [117] "SCORE" "SEQUENCE" [119] "3D" "TAXON" [121] "TOOLS" "VERSION" [123] "DATABASE(PFAM)" "DATABASE(PDB)"
-----------利用可能なkeytype--------------------
> keytypes(tmp)
[1] "UNIPROTKB" "UNIPARC" "UNIREF50"
[4] "UNIREF90" "UNIREF100" "EMBL/GENBANK/DDBJ"
[7] "EMBL/GENBANK/DDBJ_CDS" "PIR" "UNIGENE"
[10] "ENTREZ_GENE" "GI_NUMBER*" "REFSEQ_PROTEIN"
[13] "REFSEQ_NUCLEOTIDE" "PDB" "DISPROT"
[16] "HSSP" "DIP" "MINT"
[19] "ALLERGOME" "MEROPS" "PEROXIBASE"
[22] "PPTASEDB" "REBASE" "TCDB"
[25] "PHOSSITE" "DMDM" "AARHUS/GHENT-2DPAGE"
[28] "ECO2DBASE" "WORLD-2DPAGE" "DNASU"
[31] "ENSEMBL" "ENSEMBL_PROTEIN" "ENSEMBL_TRANSCRIPT"
[34] "ENSEMBL_GENOMES" "ENSEMBL_GENOMES PROTEIN" "ENSEMBL_GENOMES TRANSCRIPT"
[37] "KEGG" "PATRIC" "TIGR"
[40] "UCSC" "VECTORBASE" "AGD"
[43] "ARACHNOSERVER" "CGD" "CONOSERVER"
[46] "CYGD" "DICTYBASE" "ECHOBASE"
[49] "ECOGENE" "EUHCVDB" "EUPATHDB"
[52] "FLYBASE" "GENECARDS" "GENEFARM"
[55] "GENOLIST" "H-INVDB" "HGNC"
[58] "HPA" "LEGIOLIST" "LEPROMA"
[61] "MAIZEGDB" "MIM" "MGI"
[64] "NEXTPROT" "ORPHANET" "PHARMGKB"
[67] "POMBASE" "PSEUDOCAP" "RGD"
[70] "SGD" "TAIR" "TUBERCULIST"
[73] "WORMBASE" "WORMBASE_TRANSCRIPT" "WORMBASE_PROTEIN"
[76] "XENBASE" "ZFIN" "EGGNOG"
[79] "GENETREE" "HOGENOM" "HOVERGEN"
[82] "KO" "OMA" "ORTHODB"
[85] "PROTCLUSTDB" "BIOCYC" "REACTOME"
[88] "UNIPATHWAY" "CLEANEX" "GERMONLINE"
[91] "DRUGBANK" "GENOMERNAI" "NEXTBIO"
-------データの抽出--------------------------------------------------
UniProtのIDをキーにして、PDB番号と配列を取得する。
> select(tmp, keys=c("P31946"), columns=c("PDB","SEQUENCE"), keytype="UNIPROTKB")
Getting mapping data for P31946 ... and PDB_ID
Getting extra data for P31946 NA NA etc
UNIPROTKB PDB
1 P31946 2BQ0
2 P31946 2C23
3 P31946 4DNK
SEQUENCE
1 MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
2 MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
3 MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
---------[p.90の12番]----------------------------------------------
> O95544 <- select(tmp, keys=c("O95544"), columns=c("PDB","ENSEMBL","GO-ID","SEQUENCE"), keytype="UNIPROTKB")
Getting mapping data for O95544 ... and PDB_ID
Getting mapping data for O95544 ... and ENSEMBL_ID
Getting extra data for O95544 NA NA etc
>
> O95544
UNIPROTKB PDB ENSEMBL
1 O95544 3PFN ENSG00000008130
GO-ID
1 GO:0005524; GO:0046034; GO:0019674; GO:0003951; GO:0006741; GO:0005829; GO:0046872; GO:0016310; GO:0044281; GO:0006766; GO:0006767
SEQUENCE
1 MEMEQEKMTMNKELSPDAAAYCCSACHGDETWSYNHPIRGRAKSRSLSASPALGSTKEFRRTRSLHGPCPVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHWNVRKKQAHFEEEEEEEEEG
> O95544$SEQUENCE
[1] "MEMEQEKMTMNKELSPDAAAYCCSACHGDETWSYNHPIRGRAKSRSLSASPALGSTKEFRRTRSLHGPCPVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKMRDASLLQPFKELCTHLMEENMIVYVEKKVLEDPAIASDESFGAVKKKFCTFREDYDDISNQIDFIICLGGDGTLLYASSLFQGSVPPVMAFHLGSLGFLTPFSFENFQSQVTQVIEGNAAVVLRSRLKVRVVKELRGKKTAVHNGLGENGSQAAGLDMDVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASMIHPNVPAIMITPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDWFESLAQCLHWNVRKKQAHFEEEEEEEEEG"
=============[p.92]======================================
＜Protein Sequence解析＞
http://thegrantlab.org/bio3d/index.php
> install.packages("bio3d")
Installing package into ‘C:/Users/ekaminuma/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/bio3d_2.2-4.zip'
Content type 'application/zip' length 2740772 bytes (2.6 MB)
downloaded 2.6 MB
package ‘bio3d’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\ekaminuma\AppData\Local\Temp\Rtmp0qzd6i\downloaded_packages
>
> library(bio3d)
Warning message:
パッケージ ‘bio3d’ はバージョン 3.2.3 の R の下で造られました
=======[p.93]===============================
＜Protein sequence alignment＞
> library(muscle) 以前利用したライブラリ
> pdb1<-read.pdb("1BG2")
Note: Accessing on-line PDB file
HEADER MOTOR PROTEIN 04-JUN-98 1BG2
> pdb2<-read.pdb("2VVG")
Note: Accessing on-line PDB file
HEADER MOTOR PROTEIN 08-JUN-08 2VVG
>
> pdb3<-read.pdb("1MKJ")
Note: Accessing on-line PDB file
HEADER TRANSPORT PROTEIN 29-AUG-02 1MKJ
> s1<- aa321(pdb1$seqres)
> s2<- aa321(pdb2$seqres)
> s3<- aa321(pdb3$seqres)
>
> s1
[1] "M" "A" "D" "L" "A" "E" "C" "N" "I" "K" "V" "M" "C" "R" "F" "R" "P"
略
> raw<- seqbind(seqbind(s1,s2),s3)
> raw
1 . . . . . . 70
seq1 MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIV
seq2 MSSDNIKVIVRCRPLNARETRENALNIIRMDEASAQVIVDPPEQEKSATQAKKVPRTFTFDAVYDQTSCN
seq3 MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIV
* * * ^ ^ * ^
1 . . . . . . 70
＜略＞
一旦、fasta形式ファイルに保存。
> write.fasta(raw,ids=c("1BG2","2VVG","1MKJ"),file="raw_pdb.fa")
> pdb_seq <-readAAStringSet("raw_pdb.fa",format="fasta")
>
> pdb_seq
A AAStringSet instance of length 3
width seq names
[1] 700 MADLAECNIKVMCRFRPLNE...------------------- 1BG2
[2] 700 MSSDNIKVIVRCRPLNARET...AKQIKNKPRINEDPKDAQI 2VVG
[3] 700 MADLAECNIKVMCRFRPLNE...------------------- 1MKJ
>
> pdb_aln <- muscle(pdb_seq,out=NULL,quiet=FALSE)
Option -out must have value
Invalid option "out"
MUSCLE v3.8.31 by Robert C. Edgar
http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
Basic usage
muscle -in <inputfile> -out <outputfile>
Common options (for a complete list please see the User Guide):
-in <inputfile> Input file in FASTA format (default stdin)
-out <outputfile> Output alignment in FASTA format (default stdout)
-diags Find diagonals (faster for similar sequences)
-maxiters <n> Maximum number of iterations (integer, default 16)
-maxhours <h> Maximum time to iterate in hours (default no limit)
-html Write output in HTML format (default FASTA)
-msf Write output in GCG MSF format (default FASTA)
-clw Write output in CLUSTALW format (default FASTA)
-clwstrict As -clw, with 'CLUSTAL W (1.81)' header
-log[a] <logfile> Log to file (append if -loga, overwrite if -log)
-quiet Do not write progress messages to the screen
-version Display version information and exit
Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags
file141c35174058 3 seqs, max length 700, avg length 458
181 MB(1%)00:00:00 Iter 1 100.00% K-mer dist pass 1
181 MB(1%)00:00:00 Iter 1 100.00% K-mer dist pass 2
181 MB(1%)00:00:00 Iter 1 100.00% Align node
181 MB(1%)00:00:00 Iter 1 100.00% Root alignment
181 MB(1%)00:00:00 Iter 2 100.00% Root alignment
181 MB(1%)00:00:00 Iter 3 100.00% Refine biparts
181 MB(1%)00:00:00 Iter 4 100.00% Refine biparts
181 MB(1%)00:00:00 Iter 5 100.00% Refine biparts
181 MB(1%)00:00:00 Iter 6 100.00% Refine biparts
181 MB(1%)00:00:00 Iter 7 100.00% Refine biparts
>
> AAStr <- as(pdb_aln,"AAStringSet")
> writeXStringSet(AAStr,file="pdb_aln.fa")
> tmpdat <- read.fasta(file="pdb_aln.fa")
AAStrでなくid+seq形式のtmpdat作成
> aln2html(tmpdat,append=FALSE,file="pdb_aln.html")
pdb_aln.faとpdb_aln.htmlは添付ファイル参照
=======[p.95]===============================
＜Amino Acid Composition＞
> install.packages("protr")
>
> library(bio3d)
> library(protr)
Warning message:
パッケージ ‘protr’ はバージョン 3.2.3 の R の下で造られました
>
> pdb1 <- read.pdb("1BG2")
Note: Accessing on-line PDB file
HEADER MOTOR PROTEIN 04-JUN-98 1BG2
> s1 <- aa321(pdb1$seqres)
>
> s1 <- paste(s1,sep="",collapse="")
> s1
[1] "MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI"
> library(seqinr)
> s1tmp <- c2s(s1)
> s1tmp
[1] "MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI"
------[1.アミノ酸組成の取得]----------------------
> s1_aac <- extractAAC(s1tmp)
> s1_aac
A R N D C E Q
0.04923077 0.04307692 0.05846154 0.06153846 0.02461538 0.07384615 0.03384615
G H I L K M F
0.06153846 0.02153846 0.06769231 0.06769231 0.07692308 0.02461538 0.03384615
P S T W Y V
0.02461538 0.09538462 0.06153846 0.00000000 0.04307692 0.07692308
------[2.クエリ配列が20種類アミノ酸持つか]-----------
> s1_check <- protcheck(s1tmp)
>
> s1_check
[1] TRUE
------[3.疎水性/親水性アミノ酸(hydrophobic/hydrophilic)]---
> s1_apaac <- extractAPAAC(s1tmp,props=c("Hydrophobicity","Hydrophilicity"),lambda=30,w=0.05,customprops=NULL)
>
> s1_apaac
Pc1.A Pc1.R Pc1.N
1.559274e+01 1.364365e+01 1.851638e+01
Pc1.D Pc1.C Pc1.E
1.949093e+01 7.796371e+00 2.338911e+01
Pc1.Q Pc1.G Pc1.H
1.072001e+01 1.949093e+01 6.821824e+00
Pc1.I Pc1.L Pc1.K
2.144002e+01 2.144002e+01 2.436366e+01
Pc1.M Pc1.F Pc1.P
7.796371e+00 1.072001e+01 7.796371e+00
Pc1.S Pc1.T Pc1.W
3.021094e+01 1.949093e+01 0.000000e+00
Pc1.Y Pc1.V Pc2.Hydrophobicity.1
1.364365e+01 2.436366e+01 -2.191252e-03
Pc2.Hydrophilicity.1 Pc2.Hydrophobicity.2 Pc2.Hydrophilicity.2
1.807624e-03 -3.394759e-03 -4.43412
略
Pc2.Hydrophobicity.30 Pc2.Hydrophilicity.30
3.394123e-03 6.391990e-03
> extractCTDC(s1tmp) CTD composition
hydrophobicity.Group1 hydrophobicity.Group2 hydrophobicity.Group3
0.3476923 0.3569231 0.2953846
normwaalsvolume.Group1 normwaalsvolume.Group2 normwaalsvolume.Group3
0.3784615 0.3784615 0.2430769
polarity.Group1 polarity.Group2 polarity.Group3
0.3384615 0.2923077 0.3692308
polarizability.Group1 polarizability.Group2 polarizability.Group3
0.3292308 0.4276923 0.2430769
charge.Group1 charge.Group2 charge.Group3
0.1200000 0.7446154 0.1353846
secondarystruct.Group1 secondarystruct.Group2 secondarystruct.Group3
0.3907692 0.3076923 0.3015385
solventaccess.Group1 solventaccess.Group2 solventaccess.Group3
0.3815385 0.3476923 0.2707692
>
> extractCTDD(s1tmp) CTD distibution
prop1.G1.residue0 prop1.G1.residue25 prop1.G1.residue50
0.9230769 20.9230769 48.3076923
prop1.G1.residue75 prop1.G1.residue100 prop1.G2.residue0
68.3076923 99.3846154 0.6153846
prop1.G2.residue25 prop1.G2.residue50 prop1.G2.residue75
27.0769231 56.0000000 80.0000000
prop1.G2.residue100 prop1.G3.residue0 prop1.G3.residue25
99.6923077 0.3076923 22.7692308
prop1.G3.residue50 prop1.G3.residue75 prop1.G3.residue100
45.5384615 71.3846154 100.0000000
prop2.G1.residue0 prop2.G1.residue25 prop2.G1.residue50
0.6153846 25.5384615 54.1538462
prop2.G1.residue75 prop2.G1.residue100 prop2.G2.residue0
80.0000000 99.6923077 1.2307692
略
prop7.G1.residue75 prop7.G1.residue100 prop7.G2.residue0
76.0000000 100.0000000 0.9230769
prop7.G2.residue25 prop7.G2.residue50 prop7.G2.residue75
20.9230769 48.3076923 68.3076923
prop7.G2.residue100 prop7.G3.residue0 prop7.G3.residue25
99.3846154 0.3076923 28.6153846
prop7.G3.residue50 prop7.G3.residue75 prop7.G3.residue100
53.8461538 79.6923077 99.6923077
> extractDC(s1tmp) Dipeptide Composition
AA RA NA DA CA EA
0.000000000 0.003086420 0.000000000 0.000000000 0.003086420 0.003086420
QA GA HA IA LA KA
0.000000000 0.006172840 0.000000000 0.006172840 0.009259259 0.000000000
略
LV KV MV FV PV SV
0.003086420 0.009259259 0.000000000 0.003086420 0.000000000 0.003086420
TV WV YV VV
0.003086420 0.000000000 0.006172840 0.003086420
その他の関数情報
https://cran.r-project.org/web/packages/protr/vignettes/protr.pdf
=======[p.97]=============================
＜C-alpha coordinates＞
> class(pdb1)
[1] "pdb" "sse"
>
> attributes(pdb1)
$names
[1] "atom" "helix" "sheet" "seqres" "xyz" "calpha" "remark" "call"
$class
[1] "pdb" "sse"
> summary(pdb1)
Call: read.pdb(file = "1BG2")
Total Models#: 1
Total Atoms#: 2733, XYZs#: 8199 Chains#: 1 (values: A)
Protein Atoms#: 2527 (residues/Calpha atoms#: 323)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 206 (residues: 174)
Non-protein/nucleic resid values: [ ACT (3), ADP (1), HOH (169), MG (1) ]
+ attr: atom, helix, sheet, seqres, xyz,
calpha, remark, call
> head(pdb1$atom[,c("x","y","z")])
x y z
1 43.743 -2.106 39.408
2 45.053 -2.661 39.856
3 45.305 -2.401 41.340
4 46.119 -3.083 41.957
5 46.204 -2.067 39.034
6 45.912 -2.039 37.542
>
> head(pdb1$atom[pdb1$calpha,c("resid","elety","x","y","z")])
resid elety x y z
2 ASP CA 45.053 -2.661 39.856
10 LEU CA 44.791 -1.079 43.319
18 ALA CA 42.451 -3.691 44.790
23 GLU CA 40.334 -4.572 41.737
32 CYS CA 36.711 -3.532 42.171
38 ASN CA 36.940 -0.636 44.620
>
> write.pdb(pdb1,file="tmp_1BG2.pdb")
> read.pdb("tmp_1BG2.pdb")
Call: read.pdb(file = "tmp_1BG2.pdb")
Total Models#: 1
Total Atoms#: 2733, XYZs#: 8199 Chains#: 1 (values: A)
略
=======[p.98]============================
＜Interpro annotation＞
> library(UniProt.ws)
> tmp <- UniProt.ws(9606)
> O95544 <- select(tmp, keys=c("O95544"), columns=c("PDB","INTERPRO","GO-ID"), keytype="UNIPROTKB")
Getting mapping data for O95544 ... and PDB_ID
Getting extra data for O95544 NA NA etc
> O95544
UNIPROTKB PDB INTERPRO
1 O95544 3PFN IPR017438; IPR017437; IPR016064; IPR002504;
GO-ID
1 GO:0005524; GO:0046034; GO:0019674; GO:0003951; GO:0006741; GO:0005829; GO:0046872; GO:0016310; GO:0044281; GO:0006766; GO:0006767
http://www.uniprot.org/uniprot/O95544
======[p.100]========================
＜Ramachandran plot＞
> tor <- torsion.pdb(pdb1)
>
> plot(tor$phi,tor$psi,main="(A) Ramachandran plot 1BG2")
> scatter.psi <- tor$psi
> scatter.phi <- tor$phi
>
> library(RColorBrewer)
> k <- 10
> my.col <- rev(brewer.pal(k,"RdYlBu"))
>
> smoothScatter(x=scatter.phi,y=scatter.psi,colramp=colorRampPalette(my.col),main="(B)Ramachandran plot 1BG2",pch=19,cex=0.00)
>
======[p.102]========================
＜Searching for similar proteins＞
>
> tmpseq <- aa321(pdb1$seqres)
>
> tmpblast <- blast.pdb(tmpseq)
Searching ... please wait (updates every 5 seconds) RID = 727A1WY101N
Reporting 233 hits
>
> head(tmpblast$hit.tbl)
queryid subjectids identity positives alignmentlength
[1,] "unnamed" "gi|24987772|pdb|1MKJ|A" "100.000" "100.00" "325"
[2,] "unnamed" "gi|157830287|pdb|1BG2|A" "100.000" "100.00" "325"
[3,] "unnamed" "gi|193885175|pdb|2P4N|K" "100.000" "100.00" "325"
[4,] "unnamed" "gi|731187722|pdb|3J8X|K" " 99.077" " 99.08" "325"
[5,] "unnamed" "gi|731187725|pdb|3J8Y|K" " 99.077" " 99.08" "325"
[6,] "unnamed" "gi|406855617|pdb|4ATX|C" " 98.769" " 99.38" "325"
mismatches gapopens q.start q.end s.start s.end evalue bitscore
[1,] " 0" " 0" " 1" "325" " 1" "325" " 0.00e+00" "677.0"
[2,] " 0" " 0" " 1" "325" " 1" "325" " 0.00e+00" "675.0"
[3,] " 0" " 0" " 1" "325" " 1" "325" " 0.00e+00" "675.0"
[4,] " 3" " 0" " 1" "325" " 1" "325" " 0.00e+00" "669.0"
[5,] " 3" " 0" " 1" "325" " 1" "325" " 0.00e+00" "669.0"
> top.hits <- plot(tmpblast)
* Possible cutoff values: 709 -2
Yielding Nhits: 22 233
* Chosen cutoff value of: 709
Yielding Nhits: 22
> head(top.hits$hits)
pdb.id gi.id group
1 "1MKJ_A" "24987772" "1"
2 "1BG2_A" "157830287" "1"
3 "2P4N_K" "193885175" "1"
4 "3J8X_K" "731187722" "1"
5 "3J8Y_K" "731187725" "1"
6 "4ATX_C" "406855617" "1"
======[p.105]========================
＜Working with the secondary structure features of proteins＞
Secondary structure(SS)
http://www.rcsb.org/pdb/files/ss.txt
読み込みエラーになるのでソフトウェアを直接利用。
======[p.105]========================
＜3D Visualization＞
R2.2.3ではサポートしておらず。
インストールエラーになるので、視覚化ソフトウェアを直接利用。
