0703 choose system
待选化合物:
TCMID-27473：
结构
- # 172.21.85.12 /home/zjxu/zzy/hsbd/dock/d3S-36mol/0702-2pro/analysis
- (base) [zjxu@R820 analysis]$ sort -t ";" -k 5,5n result.txt |head -n 100|awk -F ';' '{print $2}' |sort|uniq
- TCMID-19532
- TCMID-27473
- TCMID-27701
- TCMID-27710
- TCMID-28188
- TCMID-28199
- TCMID-28201
- TCMID-28203
- TCMID-28205
- TCMID-28206
- TCMID-28223
- # 17.21.85.2 /home/dddc/zzy/test/visualize/0701-hsbd
- for i in
`cat 11mol-from100-docking`;do grep $i name-36.csv >>11mol-from100-docking.csv;done
D3Docking
- # 172.21.85.12 /home/zjxu/zzy/hsbd/dock/d3S-36mol/0702-2pro/analysis
- sort -t ";" -k 5,5n result.txt |head|awk -F ';' '{print $2}' |sort|uniq
TCMID-27473
- (base) [zjxu@R820 analysis]$ sort -t ";" -k 5,5n result.txt|grep -n TCMID-27473
- 69:ORF1ab_819-2763_Papain-like_proteinase+Dimer; TCMID-27473; Pocket2; score; -10.53
- 71:ORF1ab_819-2763_Papain-like_proteinase+Dimer; TCMID-27473; Pocket3; score; -10.52
- # 对比下最高打分，差的不算远，-10 也够高了
- (base) [zjxu@R820 analysis]$ sort -t ";" -k 5,5n result.txt|head
- ORF1ab_3264-3569_3C-like_proteinase+Dimer; TCMID-19532; Pocket1; score; -14.00
- ORF1ab_3264-3569_3C-like_proteinase+Dimer; TCMID-19532; Pocket2; score; -13.97
TCMID-27701
- sort -t ";" -k 5,5n result.txt|grep -n TCMID-27701|awk -F ';' '{print $1,$2,$4,$5}' >TCMID-27701.txt
- # 手动把非SARS2晶体结构来源的都去除了 ( MD保留了 )
- 92:Papain-like_proteinase+Trimer+6W9C TCMID-27701 score -10.1330862
- 141:3C_like_proteinase+Dimer+6Y2G TCMID-27701 score -9.54864216
- 218:3C-like_proteinase+MD1 TCMID-27701 score -8.91034126
- 253:Papain-like_proteinase+Trimer+6W9C TCMID-27701 score -8.71341991
- 280:Papain-like_protease+Monomer+6W9C TCMID-27701 score -8.58899498
- 283:3C-like_proteinase+MD3 TCMID-27701 score -8.57742691
- 311:Papain-like_proteinase+Trimer+6W9C TCMID-27701 score -8.48116493
- 313:3C-like_proteinase+MD2 TCMID-27701 score -8.46159458
- 348:3C-like_proteinase+MD2 TCMID-27701 score -8.31657696
- 442:3C-like_proteinase+MD4 TCMID-27701 score -7.80716276
- 463:Papain-like_protease+Monomer+6W9C TCMID-27701 score -7.70911789
- 465:Papain-like_proteinase+Trimer+6W9C TCMID-27701 score -7.70174503
- 498:Papain-like_protease+Monomer+6W9C TCMID-27701 score -7.57816124
- 500:3C-like_proteinase+MD3 TCMID-27701 score -7.57605219
- 520:3C-like_proteinase+MD1 TCMID-27701 score -7.44089365
- 522:3C-like_proteinase+MD4 TCMID-27701 score -7.43612957
- 529:3C-like_proteinase+MD1 TCMID-27701 score -7.36268377
- 537:3C-like_proteinase+MD4 TCMID-27701 score -7.30941534
- 570:3C-like_proteinase+MD4 TCMID-27701 score -7.06679773
- 581:3C-like_proteinase+MD3 TCMID-27701 score -6.95603657
- 587:Papain-like_proteinase+Trimer+6W9C TCMID-27701 score -6.92436743
- # 我觉得有点意思，这么看，这个化合物有可能和新冠的 PL,3CL都有结合，这样复合物的 MD 甚至有 天然 的多 初始构象
- # 对比下最高打分，差的不算远，-10 也够高了
- (base) [zjxu@R820 analysis]$ sort -t ";" -k 5,5n result.txt|head
- ORF1ab_3264-3569_3C-like_proteinase+Dimer; TCMID-19532; Pocket1; score; -14.00
- ORF1ab_3264-3569_3C-like_proteinase+Dimer; TCMID-19532; Pocket2; score; -13.97
相似性
- # 172.21.85.12 /home/zjxu/zzy/hsbd/dock/d3S-36mol/0702-2pro/analysis/check-d3S
TCMID-27473
- # 和目前报道的阳性化合物结构并非完全一致
- target2 TCMID-27473 ICV283 0.913043 0.64787
- target2 TCMID-27473 ICV713 0.962963 0.60831
TCMID-27701
- # 阳性化合物 ICV369（补骨脂色烯查耳酮）与该化合物的骨架完全一致，但不是一个化合物
- (base) [zjxu@R820 check-d3S]$ grep TCMID-27701 d3S-result.txt
- target1 TCMID-27701 ICV369 1 0.74712 0.74712
- target2 TCMID-27701 ICV369 1 0.74712 0.74712
AI
TCMID-27473
- # 172.21.85.3 /home/yqyang/zzy/hsbd/d3ai-cov
- grep TCMID-27473 workdir/*/* >TCMID-27473
- awk -F '|' '{print $2,$4,$5}' TCMID-27473|sort -k 3
- # 对接的受体，SARS_Pap 的分数最高（非SARS2_Pap）
- # 该结果与受体结构相呼应（对接的受体并非真的SARS2结构，而是根据SARS同源建模而来）
TCMID-27701
- # 172.21.85.3 /home/yqyang/zzy/hsbd/d3ai-cov
- grep TCMID-27701 workdir/*/* |awk -F '|' '{print $2,$4,$5}' |sort -k 3
- 853 SARS2_3C 0.39481
- 338 SARS_Pap 0.84910
结合模式及受体蛋白
TCMID-27473
- cp /home/zjxu/xbzhang/2019-nCov-final/preparation/protein-v1/ORF1ab_819-2763_Papain-like_proteinase+Dimer.pdbqt ./
- cp ../../dock-conf/TCMID-27473/ORF1ab_819-2763_Papain-like_proteinase+Dimer-TCMID-27473-pkt2-0.sdf ./
- cp ../../dock-conf/TCMID-27473/ORF1ab_819-2763_Papain-like_proteinase+Dimer-TCMID-27473-pkt3-0.sdf ./
- ### 对接对应的蛋白非晶体结构
TCMID-27701
- cp /home/zjxu/xbzhang/2019-nCov-final/preparation/protein-v1/Papain-like_proteinase+Trimer+6W9C.pdbqt ./
- cp ../../dock-conf/TCMID-27701/Papain-like_proteinase+Trimer+6W9C-TCMID-27701-pkt3-0.sdf ./
- cp /home/zjxu/xbzhang/2019-nCov-final/preparation/protein-v1/3C_like_proteinase+Dimer+6Y2G.pdbqt ./
- cp ../../dock-conf/TCMID-27701/3C_like_proteinase+Dimer+6Y2G-TCMID-27701-pkt2-0.sdf ./
- cp /home/zjxu/xbzhang/2019-nCov-final/preparation/protein-v1/Papain-like_protease+Monomer+6W9C.pdbqt ./
- cp ../../dock-conf/TCMID-27701/Papain-like_protease+Monomer+6W9C-TCMID-27701-pkt5-0.sdf ./
- cp /home/zjxu/xbzhang/2019-nCov-final/preparation/protein-v1/3C-like_proteinase+MD1.pdbqt ./
- cp ../../dock-conf/TCMID-27701/3C-like_proteinase+MD1-TCMID-27701-pkt2-0.sdf ./