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damlab
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HIV_V3_coreceptor

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train · 2.94k rows

sequence stringlengths 1 38	id stringlengths 6 8	CXCR4 bool 2 classes	CCR5 bool 2 classes	fold int32 0 4
CARPFYAIERQKTPIGQGQVLYTTKKIGRIGQAHC	U08806	true	false	3
CARPFYAIERQRTPIGQGQVLYTTKKIGRIGQAHC	U08734	true	false	4
CARPFYAIERQXTPIGQGQVLYTTKKIGRIGQAHC	AY669759	true	false	4
CARPGNKTRQSIRIHRGPGRAFYTTKATGDIRKAQC	MZ147126	true	false	0
CARPGNKTRQSIRIHRGPGRAFYTTNAGDIRKAHC	MZ147128	true	false	1
CARPGNNTIKRIRIGPRYAFYAKETIIGDIRQAHC	AF411967	true	true	1
CARPGNNTKKSVRIGPGQTFYATGDIIGDIRQAHC	FJ977091	false	true	1
CARPGNNTRKMMRIGIGRGQTFYANGQVIGDIRQAHC	AY529678	true	false	2
CARPGNNTRKSIRIGPGQTFFATGAIIGDIRQAHC	L22956	true	false	3
CARPGNNTRKSVRIGPGQAFYATGDIIGDIRQAHC	FJ977094	false	true	4
CARPGNNTRKSVRIGPGQTFFATGDIIGDIRKAHC	DQ382364	false	true	4
CARPGNNTRKSXRIGPGQSFHATGEIIGNIREAHC	FJ376003	false	true	2
CARPGNNTRRSISIGPGRAFFATGDIIGDIRQAHC	MG186797	false	true	2
CARPGNNTRRSVRIGPGQAFYATGEIIGDIRKAHC	DQ382371	false	true	0
CARPHNNTRKSIHIGPGRAFYATGQITGDIRQAYC	AJ418534	false	true	0
CARPHNNTRKSMRIGPGQAFYATGDVTGDIRQAHC	KC156330	false	true	4
CARPNNNTRKGIHIGPGRAFYTTGEIIGDIRQAHC	JF508037	false	true	0
CARPNNNTRKGIHMGPGRAMYATEKITGDIRQAHC	AY842826	true	false	1
CARPNNNTRKHVRIGIGRGQTFYATGAIIGDIRQAHC	DQ382373	true	true	2
CARPNNNTRKRIYMGTGRYMSATEKITGDIRQAHC	AY842825	true	true	0
CARPNNNTRKRIYMGTGRYMSATEKITGDIRQARC	AY842833	true	false	3
CARPNNNTRKSIHIAPGRAFHTTGSIIGDIRKAYC	GU204920	false	true	4
CARPNNNTRKSIHIAPGRAFYTTGSIIGDIRQAHC	GU204919	false	true	2
CARPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHC	DQ061436	false	true	2
CARPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC	AF153130	false	true	3
CARPNNNTRKSIRIGPGQAFYATGEIIGNIRQAHC	DQ235622	false	true	3
CARPNNNTRKSIRIGPGQTFYATNDIIGNIRQAHC	AY887874	false	true	0
CARPNNNTRKSMRIGPGQAFYATGEIIGNIREAHC	HM179732	false	true	1
CARPNNNTRKSMRIGPGQTFYATGDIIGDIRQAHC	AY713416	false	true	3
CARPNNNTRKSVRIGPGQTFYATGGIIGDIRQAHC	AY170662	false	true	0
CARPNNNTRRGINIGPGRAFYATGEIIGDIRQAYC	MG184247	false	true	3
CARPNNNTRRSISIGPGRAFYTTGDIIGDIRQAHC	MG185496	false	true	2
CARPNNNTRRSISMGPGRTLYATGQIIGDIRQAHC	MG184121	false	true	3
CARPNNNTRRSITIGPGRAFYATDIIGDIRKAHC	DQ002183	false	true	4
CARPNNNTRTSVRIGPGQAFYATNDIIGKIRQAHC	AY170666	false	true	1
CARPNNSTRKGIHIGPGRAFYAAADIIGDIRQAHC	DQ869023	false	true	3
CARPNXYTRQRIGIGRGQALFTARRIIGNIKQAHC	FJ375993	true	false	3
CARPSNNTRKSIRIGPGQTFYATGEIIGDIRQAHC	EU622005	false	true	3
CARPSNNTRKSITIGPGRAFYATGDIIEDIRKAHC	DQ002227	false	true	2
CARPSNNTRTSIRIGPGQTFYATGAITGDIRQAHC	EF117271	false	true	1
CARPYIKIWRRTHIGSGQAYSTKRIQNYTGPAHC	AY669756	true	false	3
CARPYNNTRQGTHIGPGQAYFTTNIVGDIRQAHC	AY669750	false	true	4
CARPYNNTRRGTHIGPGQAYFTTKIIGDIRQAHC	EF575431	true	true	2
CARPYQNTRQRTPIGLGQSLYTTRSRSIIGQAHC	K03454	true	false	3
CERPGNNTRKSVRIGPGQTFYATGEIIGNIRQAHC	AF153157	false	true	4
CERPGNNTSKGIHIGPGRAFCATENIIGDIRKAHC	EF579978	false	true	1
CERPGNNTSKGIHIGPGRAFYATEDIIGDIRKAHC	EF579990	false	true	4
CERPGNNTSKGIHIGPGRAFYATENIIGDIRKAHC	EF579969	false	true	0
CERPGNNTSKGIHIGPGRAFYATENIIGDIRKARC	EF579987	false	true	4
CERPGNNTSKGIHIGPGRAFYATENIVGDIRKAHC	EF579993	false	true	1
CERPGNNTSKGIHIGPGRAFYATVNIIGDIRKAHC	EF579976	false	true	1
CERPGNNTSKGIHRTRESILCNRKCNRRYKKSTL	EF579986	false	true	4
CERPNNNTIKSIHLGPGRAWHATGQIIGDIRKAFC	AY835443	false	true	1
CERPNNNTRKGIAIGPGRVVYATEKIIGNIRRAHC	JF507777	true	true	4
CERPNNNTRKGIHIGPGRTFFATGEIIGDIRRAYC	JF507768	false	true	0
CERPNNNTRKGIHIGPGRVFFATGEVIGDIRRAYC	JF507761	true	true	1
CERPNNNTRKGIHIGPGRVFYATGEIIGDIRKAHC	JF507755	true	true	0
CERPNNNTRKGIHIGPGRVFYATGEIIGDIRRAHC	JF507726	true	true	0
CERPNNNTRKGIHIGPGRVFYATGGIIGDIRRAHC	JF507735	true	true	4
CERPNNNTRKGISIGPGRVVYATEKIIGNIRRAHC	JF507786	true	true	0
CERPNNNTRKSIHIAPGRTFYATGEIIGNIRQAHC	HM239570	false	true	4
CERPNNNTRKSIHIGPGRAFYTTGAIIGDIRKAHC	HQ678296	true	true	2
CERPNNNTRKSIHLGPGGAFYATGNIIGDIRKAHC	KP693372	false	true	3
CERPNNNTRKSIHLGPGGAFYATGRIIGDIRKAHC	KP693375	false	true	1
CERPNNNTRKSIPIGPGRVFFATGGIIGDIRRAHC	JF507744	true	true	2
CERPNNNTRKSIRIGPGSAFYAAGEIIGNIRQAHC	KC312573	false	true	2
CERPNNNTRKSIRIGPGSAFYATGEIIGNIRQAHC	KC312590	false	true	4
CERPNNNTRKSIRIGPGSTFYATGEIIGNIRQAHC	KC312574	false	true	3
CERPNNNTRKSVHIGPGQAFYATGSIIGDIRAAYC	HF571996	false	true	4
CERPNNNTRQGIHIGPGKAYFTTNIIGDIRSAHC	KP109501	true	true	2
CERPNNNTRQSIHIGPGQAIYANEKIIGDIRQAHC	HQ906872	false	true	2
CERPNNNTRRSIHIGPGRAFYAGEIIGNIRKAYC	EU575148	false	true	4
CERPNNNTRRSIPIGPGRVFFTSEIIGDIRQAYC	KF384811	false	true	4
CERPNNNTRRSIQIGPGRAWFEAEDIIGDIRKAHC	AB553911	false	true	2
CERPNNNTRSSIHIGPGRSLYTTDIIGDIRNAYC	JX140670	true	true	1
CERTNNNTRKSIHIGPGQALYATTNIIGDIRKAHC	HM239528	false	true	3
CERTNNNTRKSIHIGPGQALYATTNIIGDIRNAHC	HQ906864	false	true	2
CERXNDNKRQSIHJGPGQAIYTNKXIGDIRQAXC	HQ906870	false	true	1
CGRPGNNTSKGIHMGPGRAFYATENIIGDIRKAHC	EF579975	false	true	4
CGRPNNHRIKGLRIGPGRAFFAMGAIGGGEIRQAHC	AY265949	true	false	1
CGRPNNHRIKGLRIGPGRAFFAMGAIRGGEIRQAHC	FJ541295	true	false	0
CIKPNNNTRKSINIGPGRAFYAADQIIGDIRQAHC	MG187077	false	true	1
CIKPNNNTRKSIPIGPGKAWYTTGQIIRDIRRAHC	EU272220	false	true	2
CIRIGNNTRKSVRIGPGQVFFANDIIGDIRQAHC	MT222960	false	true	1
CIRPDNNTRKSIRIGPGQTFYATGDIIGNIRKAYC	HQ708020	false	true	2
CIRPDNNTRRSIRIGPGQVFYANDIIGDIREASC	KF770313	false	true	1
CIRPFYKTRKSVRVGLGRAYLTERIRGDIRQAHC	AM156912	true	false	2
CIRPGINKRKRIRIGLRYAFFATDNRIGKAHC	AY887865	false	true	1
CIRPGNKKIRSXRIGPGRXFXATGGDIRKAYC	FJ376008	true	true	1
CIRPGNKTRKSMRIGRGHTFYATGKIIGDIRKAHC	KF770278	true	true	4
CIRPGNNMRKSVRIGPGQAFYATGDIIGDIRQAHC	JX973084	false	true	1
CIRPGNNTGKSIPMGPGRAWYATGSIIGDIRQAHC	AF384257	false	true	2
CIRPGNNTKKFIHLGPRRAFYATHNIGDARQAHC	MG188247	true	true	4
CIRPGNNTKRFIHLGPRRAFYATHNIGDARQAHC	MG188251	true	false	0
CIRPGNNTRKGMRIGPGQTFYATGDIIGDIRQAHC	AF153165	false	true	4
CIRPGNNTRKGMRIGPGQTFYATGEIIGDIRQAHC	KF770331	false	true	1
CIRPGNNTRKRVRLGIGPGQTFYATGRVIRDIRQAHC	AY529666	true	true	2
CIRPGNNTRKSIHIAPGRAFYATGDIIGDIRQAHC	HQ678293	false	true	1
CIRPGNNTRKSIHIGPGRAFYATGDIIGDIRQAHC	HQ644857	false	true	1
CIRPGNNTRKSIHIGPGRAFYATGNIIGDIRQAHC	HM239618	false	true	3

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Dataset Description

Dataset Summary

This dataset was derived from the Los Alamos National Laboratory HIV sequence (LANL) database. It contains 2,935 HIV V3 loop protein sequences, which can interact with either CCR5 receptors on T-Cells or CXCR4 receptors on macrophages.

Supported Tasks and Leaderboards: None

Languages: English

Dataset Structure

Data Instances

Data Instances: Each column represents the protein amino acid sequence of the HIV V3 loop. The ID field indicates the Genbank reference ID for future cross-referencing. There are 2,935 total V3 sequences, with 91% being CCR5 tropic and 23% CXCR4 tropic. Data Fields: ID, sequence, fold, CCR5, CXCR4 Data Splits: None

Dataset Creation

Curation Rationale: This dataset was curated to train a model (HIV-BERT-V3) designed to predict whether an HIV V3 loop would be CCR5 or CXCR4 tropic.

Initial Data Collection and Normalization: Dataset was downloaded and curated on 12/20/2021.

Considerations for Using the Data

Social Impact of Dataset: This dataset can be used to study the mechanism by which HIV V3 loops allow for entry into T-cells and macrophages.

Discussion of Biases: Due to the sampling nature of this database, it is predominantly composed of subtype B sequences from North America and Europe with only minor contributions of Subtype C, A, and D. Currently, there was no effort made to balance the performance across these classes. As such, one should consider refinement with additional sequences to perform well on non-B sequences.

Additional Information:

Dataset Curators: Will Dampier
Citation Information: TBA

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Size of downloaded dataset files:

59.2 kB

Size of the auto-converted Parquet files:

59.2 kB

Number of rows:

2,935