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deepmodeling / Uni-Mol

Official Repository for the Uni-Mol Series Methods
MIT License
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您好，请问可以提供原始口袋的pdb文件吗 #235

Open lmqfly opened 4 weeks ago

ZhouGengmo commented 4 weeks ago

请问这里说的是什么口袋

lmqfly commented 3 weeks ago

我可以获得dpocket检测出来的口袋的pdb文件吗

Original

From:"ZhouGengmo"< @.*** >;

Date:2024/6/21 13:54

To:"dptech-corp/Uni-Mol"< @.*** >;

CC:"MQ Liu"< @. >;"Author"< @. >;

Subject:Re: [dptech-corp/Uni-Mol] 您好，请问可以提供原始口袋的pdb文件吗 (Issue #235)

请问这里说的是什么口袋

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ZhouGengmo commented 3 weeks ago

是fpocket提取的用于预训练的口袋pdb吗，比如下面这个，这个数量比较多。 如果确定是这个的话这边需要整理一下

HEADER HEADER This is a pdb format file writen by the programm fpocket.
HEADER It represents the atoms contacted by the voronoi vertices of the pocket.
HEADER
HEADER Information about the pocket 1: HEADER 0 - Pocket Score : 0.0639 HEADER 1 - Drug Score : 0.0002 HEADER 2 - Number of alpha spheres : 15 HEADER 3 - Mean alpha-sphere radius : 4.0407 HEADER 4 - Mean alpha-sphere Solvent Acc. : 0.6711 HEADER 5 - Mean B-factor of pocket residues : 0.0000 HEADER 6 - Hydrophobicity Score : 20.4000 HEADER 7 - Polarity Score : 2 HEADER 8 - Amino Acid based volume Score : 3.0000 HEADER 9 - Pocket volume (Monte Carlo) : 276.2768 HEADER 10 -Pocket volume (convex hull) : 10.3043 HEADER 11 - Charge Score : 0 HEADER 12 - Local hydrophobic density Score : 6.0000 HEADER 13 - Number of apolar alpha sphere : 7 HEADER 14 - Proportion of apolar alpha sphere : 0.4667 ATOM 2112 CG ASN A 132 23.770 16.739 0.357 0.00 0.00 C 0 ATOM 2114 OD1 ASN A 132 23.803 15.923 1.265 0.00 0.00 O 0 ATOM 1829 CD1 ILE A 112 26.396 17.872 4.128 0.00 0.00 C 0 ATOM 2063 NE2 GLN A 128 24.140 22.445 4.081 0.00 0.00 N 0 ATOM 2111 CB ASN A 132 24.925 17.699 0.156 0.00 0.00 C 0 ATOM 2113 ND2 ASN A 132 22.777 16.796 -0.521 0.00 0.00 N 0 ATOM 2074 CA GLY A 129 25.088 21.443 -2.354 0.00 0.00 C 0 ATOM 2064 OE1 GLN A 128 25.372 24.311 3.925 0.34 7.50 O 0 ATOM 2062 CD GLN A 128 25.069 23.195 3.504 0.00 0.00 C 0 ATOM 2028 CB ALA A 125 23.600 27.970 -1.090 0.00 0.00 C 0 ATOM 2025 CA ALA A 125 24.917 27.259 -0.746 0.00 0.00 C 0 ATOM 2061 CG GLN A 128 25.765 22.583 2.295 0.00 0.00 C 0 ATOM 2059 O GLN A 128 26.579 20.692 -0.161 0.00 0.00 O 0 ATOM 2027 O ALA A 125 25.058 25.124 -1.837 0.00 0.00 O 0 ATOM 2060 CB GLN A 128 26.479 23.596 1.390 0.00 0.00 C 0 ATOM 2073 N GLY A 129 25.861 22.348 -1.516 0.00 0.00 N 0 TER END