biodatasets/afdb_e_coli
收藏Hugging Face2024-11-14 更新2025-11-15 收录
下载链接:
https://hf-mirror.com/datasets/biodatasets/afdb_e_coli
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资源简介:
---
dataset_info:
- config_name: array
features:
- name: name
dtype: string
- name: structure
struct:
- name: coords
dtype:
array2_d:
shape:
- null
- 3
dtype: float16
- name: restype_index
dtype:
array1_d:
shape:
- null
dtype: uint8
- name: chain_id
dtype:
array1_d:
shape:
- null
dtype: string
- name: b_factor
dtype:
array1_d:
shape:
- null
dtype: float16
splits:
- name: train
num_bytes: 232476354.0
num_examples: 8726
download_size: 119713209
dataset_size: 232476354.0
bio_features:
- name: name
dtype: string
- name: structure
dtype:
protein_atom_array_feature:
residue_dictionary:
residue_names:
- ALA
- ARG
- ASN
- ASP
- CYS
- GLN
- GLU
- GLY
- HIS
- ILE
- LEU
- LYS
- MET
- PHE
- PRO
- SER
- THR
- TRP
- TYR
- UNK
- VAL
residue_letters:
- A
- R
- N
- D
- C
- Q
- E
- G
- H
- I
- L
- K
- M
- F
- P
- S
- T
- W
- Y
- X
- V
residue_atoms:
ALA:
- N
- CA
- C
- O
- CB
ARG:
- N
- CA
- C
- O
- CB
- CG
- CD
- NE
- CZ
- NH1
- NH2
ASN:
- N
- CA
- C
- O
- CB
- CG
- OD1
- ND2
ASP:
- N
- CA
- C
- O
- CB
- CG
- OD1
- OD2
CYS:
- N
- CA
- C
- O
- CB
- SG
GLN:
- N
- CA
- C
- O
- CB
- CG
- CD
- OE1
- NE2
GLU:
- N
- CA
- C
- O
- CB
- CG
- CD
- OE1
- OE2
GLY:
- N
- CA
- C
- O
HIS:
- N
- CA
- C
- O
- CB
- CG
- ND1
- CD2
- CE1
- NE2
ILE:
- N
- CA
- C
- O
- CB
- CG1
- CG2
- CD1
LEU:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
LYS:
- N
- CA
- C
- O
- CB
- CG
- CD
- CE
- NZ
MET:
- N
- CA
- C
- O
- CB
- CG
- SD
- CE
PHE:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- CE1
- CE2
- CZ
PRO:
- N
- CA
- C
- O
- CB
- CG
- CD
SER:
- N
- CA
- C
- O
- CB
- OG
THR:
- N
- CA
- C
- O
- CB
- OG1
- CG2
TRP:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- NE1
- CE2
- CE3
- CZ2
- CZ3
- CH2
TYR:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- CE1
- CE2
- CZ
- OH
UNK:
- N
- CA
- C
- O
- CB
- CG
VAL:
- N
- CA
- C
- O
- CB
- CG1
- CG2
residue_elements:
ALA:
- N
- C
- C
- O
- C
ARG:
- N
- C
- C
- O
- C
- C
- C
- N
- C
- N
- N
ASN:
- N
- C
- C
- O
- C
- C
- O
- N
ASP:
- N
- C
- C
- O
- C
- C
- O
- O
CYS:
- N
- C
- C
- O
- C
- S
GLN:
- N
- C
- C
- O
- C
- C
- C
- O
- N
GLU:
- N
- C
- C
- O
- C
- C
- C
- O
- O
GLY:
- N
- C
- C
- O
HIS:
- N
- C
- C
- O
- C
- C
- N
- C
- C
- N
ILE:
- N
- C
- C
- O
- C
- C
- C
- C
LEU:
- N
- C
- C
- O
- C
- C
- C
- C
LYS:
- N
- C
- C
- O
- C
- C
- C
- C
- N
MET:
- N
- C
- C
- O
- C
- C
- S
- C
PHE:
- N
- C
- C
- O
- C
- C
- C
- C
- C
- C
- C
PRO:
- N
- C
- C
- O
- C
- C
- C
SER:
- N
- C
- C
- O
- C
- O
THR:
- N
- C
- C
- O
- C
- O
- C
TRP:
- N
- C
- C
- O
- C
- C
- C
- C
- N
- C
- C
- C
- C
- C
TYR:
- N
- C
- C
- O
- C
- C
- C
- C
- C
- C
- C
- O
UNK:
- N
- C
- C
- O
- C
- C
VAL:
- N
- C
- C
- O
- C
- C
- C
unknown_residue_name: UNK
atom_types:
- N
- CA
- C
- CB
- O
- CG
- CG1
- CG2
- OG
- OG1
- SG
- CD
- CD1
- CD2
- ND1
- ND2
- OD1
- OD2
- SD
- CE
- CE1
- CE2
- CE3
- NE
- NE1
- NE2
- OE1
- OE2
- CH2
- NH1
- NH2
- OH
- CZ
- CZ2
- CZ3
- NZ
- OXT
element_types:
- C
- N
- O
- S
residue_categories:
ALA: protein
ARG: protein
ASN: protein
ASP: protein
CYS: protein
GLN: protein
GLU: protein
GLY: protein
HIS: protein
ILE: protein
LEU: protein
LYS: protein
MET: protein
PHE: protein
PRO: protein
SER: protein
THR: protein
TRP: protein
TYR: protein
UNK: protein
VAL: protein
backbone_atoms:
- N
- CA
- C
- O
conversions:
- residue: MSE
to_residue: MET
atom_swaps:
- - SE
- SD
element_swaps:
- - SE
- S
- residue: SEC
to_residue: CYS
atom_swaps:
- - SE
- SG
element_swaps:
- - SE
- S
all_atoms_present: true
load_as: chain
coords_dtype: float16
b_factor_is_plddt: true
b_factor_dtype: float16
with_element: false
with_hetero: false
with_b_factor: true
- config_name: default
features:
- name: name
dtype: string
- name: structure
struct:
- name: bytes
dtype: binary
- name: path
dtype: string
- name: type
dtype: string
splits:
- name: train
num_bytes: 43892127.0
num_examples: 8726
download_size: 43456244
dataset_size: 43892127.0
bio_features:
- name: name
dtype: string
- name: structure
dtype:
protein_structure_feature:
load_as: chain
with_b_factor: true
residue_dictionary:
residue_names:
- ALA
- ARG
- ASN
- ASP
- CYS
- GLN
- GLU
- GLY
- HIS
- ILE
- LEU
- LYS
- MET
- PHE
- PRO
- SER
- THR
- TRP
- TYR
- UNK
- VAL
residue_letters:
- A
- R
- N
- D
- C
- Q
- E
- G
- H
- I
- L
- K
- M
- F
- P
- S
- T
- W
- Y
- X
- V
residue_atoms:
ALA:
- N
- CA
- C
- O
- CB
ARG:
- N
- CA
- C
- O
- CB
- CG
- CD
- NE
- CZ
- NH1
- NH2
ASN:
- N
- CA
- C
- O
- CB
- CG
- OD1
- ND2
ASP:
- N
- CA
- C
- O
- CB
- CG
- OD1
- OD2
CYS:
- N
- CA
- C
- O
- CB
- SG
GLN:
- N
- CA
- C
- O
- CB
- CG
- CD
- OE1
- NE2
GLU:
- N
- CA
- C
- O
- CB
- CG
- CD
- OE1
- OE2
GLY:
- N
- CA
- C
- O
HIS:
- N
- CA
- C
- O
- CB
- CG
- ND1
- CD2
- CE1
- NE2
ILE:
- N
- CA
- C
- O
- CB
- CG1
- CG2
- CD1
LEU:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
LYS:
- N
- CA
- C
- O
- CB
- CG
- CD
- CE
- NZ
MET:
- N
- CA
- C
- O
- CB
- CG
- SD
- CE
PHE:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- CE1
- CE2
- CZ
PRO:
- N
- CA
- C
- O
- CB
- CG
- CD
SER:
- N
- CA
- C
- O
- CB
- OG
THR:
- N
- CA
- C
- O
- CB
- OG1
- CG2
TRP:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- NE1
- CE2
- CE3
- CZ2
- CZ3
- CH2
TYR:
- N
- CA
- C
- O
- CB
- CG
- CD1
- CD2
- CE1
- CE2
- CZ
- OH
UNK:
- N
- CA
- C
- O
- CB
- CG
VAL:
- N
- CA
- C
- O
- CB
- CG1
- CG2
residue_elements:
ALA:
- N
- C
- C
- O
- C
ARG:
- N
- C
- C
- O
- C
- C
- C
- N
- C
- N
- N
ASN:
- N
- C
- C
- O
- C
- C
- O
- N
ASP:
- N
- C
- C
- O
- C
- C
- O
- O
CYS:
- N
- C
- C
- O
- C
- S
GLN:
- N
- C
- C
- O
- C
- C
- C
- O
- N
GLU:
- N
- C
- C
- O
- C
- C
- C
- O
- O
GLY:
- N
- C
- C
- O
HIS:
- N
- C
- C
- O
- C
- C
- N
- C
- C
- N
ILE:
- N
- C
- C
- O
- C
- C
- C
- C
LEU:
- N
- C
- C
- O
- C
- C
- C
- C
LYS:
- N
- C
- C
- O
- C
- C
- C
- C
- N
MET:
- N
- C
- C
- O
- C
- C
- S
- C
PHE:
- N
- C
- C
- O
- C
- C
- C
- C
- C
- C
- C
PRO:
- N
- C
- C
- O
- C
- C
- C
SER:
- N
- C
- C
- O
- C
- O
THR:
- N
- C
- C
- O
- C
- O
- C
TRP:
- N
- C
- C
- O
- C
- C
- C
- C
- N
- C
- C
- C
- C
- C
TYR:
- N
- C
- C
- O
- C
- C
- C
- C
- C
- C
- C
- O
UNK:
- N
- C
- C
- O
- C
- C
VAL:
- N
- C
- C
- O
- C
- C
- C
unknown_residue_name: UNK
atom_types:
- N
- CA
- C
- CB
- O
- CG
- CG1
- CG2
- OG
- OG1
- SG
- CD
- CD1
- CD2
- ND1
- ND2
- OD1
- OD2
- SD
- CE
- CE1
- CE2
- CE3
- NE
- NE1
- NE2
- OE1
- OE2
- CH2
- NH1
- NH2
- OH
- CZ
- CZ2
- CZ3
- NZ
- OXT
element_types:
- C
- N
- O
- S
residue_categories:
ALA: protein
ARG: protein
ASN: protein
ASP: protein
CYS: protein
GLN: protein
GLU: protein
GLY: protein
HIS: protein
ILE: protein
LEU: protein
LYS: protein
MET: protein
PHE: protein
PRO: protein
SER: protein
THR: protein
TRP: protein
TYR: protein
UNK: protein
VAL: protein
backbone_atoms:
- N
- CA
- C
- O
conversions:
- residue: MSE
to_residue: MET
atom_swaps:
- - SE
- SD
element_swaps:
- - SE
- S
- residue: SEC
to_residue: CYS
atom_swaps:
- - SE
- SG
element_swaps:
- - SE
- S
keep_oxt: true
configs:
- config_name: array
data_files:
- split: train
path: array/train-*
- config_name: default
data_files:
- split: train
path: data/train-*
---
数据集信息:
1. 配置名称:array
特征字段:
- 字段名:name,数据类型:字符串
- 字段名:structure,为结构体类型,包含以下子字段:
- 字段名:coords(坐标),数据类型为二维数组:形状为(可变长度, 3),数据类型为半精度浮点数(float16)
- 字段名:restype_index(残基类型索引),数据类型为一维数组:形状为(可变长度),数据类型为无符号8位整数(uint8)
- 字段名:chain_id(链标识符),数据类型为一维数组:形状为(可变长度),数据类型为字符串
- 字段名:b_factor(B因子,即蛋白质结构温度因子),数据类型为一维数组:形状为(可变长度),数据类型为半精度浮点数(float16)
数据划分:
- 划分名称:训练集(train),字节占用量:232476354.0,样本数量:8726
下载总大小:119713209 字节
数据集存储总大小:232476354.0 字节
生物信息特征:
- 字段名:name,数据类型:字符串
- 字段名:structure,数据类型为蛋白质原子数组特征(protein_atom_array_feature),具体配置如下:
残基字典:
- 残基名称列表:ALA、ARG、ASN、ASP、CYS、GLN、GLU、GLY、HIS、ILE、LEU、LYS、MET、PHE、PRO、SER、THR、TRP、TYR、UNK、VAL
- 残基单字母缩写列表:A、R、N、D、C、Q、E、G、H、I、L、K、M、F、P、S、T、W、Y、X、V
残基原子映射:
ALA:N、CA、C、O、CB
ARG:N、CA、C、O、CB、CG、CD、NE、CZ、NH1、NH2
ASN:N、CA、C、O、CB、CG、OD1、ND2
ASP:N、CA、C、O、CB、CG、OD1、OD2
CYS:N、CA、C、O、CB、SG
GLN:N、CA、C、O、CB、CG、CD、OE1、NE2
GLU:N、CA、C、O、CB、CG、CD、OE1、OE2
GLY:N、CA、C、O
HIS:N、CA、C、O、CB、CG、ND1、CD2、CE1、NE2
ILE:N、CA、C、O、CB、CG1、CG2、CD1
LEU:N、CA、C、O、CB、CG、CD1、CD2
LYS:N、CA、C、O、CB、CG、CD、CE、NZ
MET:N、CA、C、O、CB、CG、SD、CE
PHE:N、CA、C、O、CB、CG、CD1、CD2、CE1、CE2、CZ
PRO:N、CA、C、O、CB、CG、CD
SER:N、CA、C、O、CB、OG
THR:N、CA、C、O、CB、OG1、CG2
TRP:N、CA、C、O、CB、CG、CD1、CD2、NE1、CE2、CE3、CZ2、CZ3、CH2
TYR:N、CA、C、O、CB、CG、CD1、CD2、CE1、CE2、CZ、OH
UNK:N、CA、C、O、CB、CG
VAL:N、CA、C、O、CB、CG1、CG2
残基元素组成映射:
ALA:N、C、C、O、C
ARG:N、C、C、O、C、C、C、N、C、N、N
ASN:N、C、C、O、C、C、O、N
ASP:N、C、C、O、C、C、O、O
CYS:N、C、C、O、C、S
GLN:N、C、C、O、C、C、C、O、N
GLU:N、C、C、O、C、C、C、O、O
GLY:N、C、C、O
HIS:N、C、C、O、C、C、N、C、C、N
ILE:N、C、C、O、C、C、C、C
LEU:N、C、C、O、C、C、C、C
LYS:N、C、C、O、C、C、C、C、N
MET:N、C、C、O、C、C、S、C
PHE:N、C、C、O、C、C、C、C、C、C、C
PRO:N、C、C、O、C、C、C
SER:N、C、C、O、C、O
THR:N、C、C、O、C、O、C
TRP:N、C、C、O、C、C、C、C、N、C、C、C、C、C
TYR:N、C、C、O、C、C、C、C、C、C、C、O
UNK:N、C、C、O、C、C
VAL:N、C、C、O、C、C、C
未知残基名称:UNK
支持的原子类型:N、CA、C、CB、O、CG、CG1、CG2、OG、OG1、SG、CD、CD1、CD2、ND1、ND2、OD1、OD2、SD、CE、CE1、CE2、CE3、NE、NE1、NE2、OE1、OE2、CH2、NH1、NH2、OH、CZ、CZ2、CZ3、NZ、OXT
支持的元素类型:C、N、O、S
残基分类:所有列示残基均为蛋白质源性残基
主链原子:N、CA、C、O
残基转换规则:
1. 残基MSE(硒代甲硫氨酸)转换为MET(甲硫氨酸):原子替换为将SE替换为SD,元素替换为将SE替换为S
2. 残基SEC(硒代半胱氨酸)转换为CYS(半胱氨酸):原子替换为将SE替换为SG,元素替换为将SE替换为S
其他配置:所有原子均已包含,加载方式为按链加载,坐标数据类型为float16,B因子即为预测局部距离差测试得分(pLDDT),B因子数据类型为float16,不包含元素信息、异质原子,包含B因子信息
2. 配置名称:default
特征字段:
- 字段名:name,数据类型:字符串
- 字段名:structure,为结构体类型,包含以下子字段:
- 字段名:bytes,数据类型:二进制数据
- 字段名:path,数据类型:字符串
- 字段名:type,数据类型:字符串
数据划分:
- 划分名称:训练集(train),字节占用量:43892127.0,样本数量:8726
下载总大小:43456244 字节
数据集存储总大小:43892127.0 字节
生物信息特征:
- 字段名:name,数据类型:字符串
- 字段名:structure,数据类型为蛋白质结构特征(protein_structure_feature),其残基字典、原子映射等配置与array配置一致,额外配置:保留末端羧基氧原子(OXT)
配置列表:
- 配置名称:array,数据文件路径:array/train-*(对应训练集划分)
- 配置名称:default,数据文件路径:data/train-*(对应训练集划分)
提供机构:
biodatasets


