🧬 BioBenchmarks v2.0.0

/ search · g then a key to jump · ? help

ProteinGym

Large-scale benchmark for protein fitness prediction from DMS + clinical variant effects.

Kind

meta-platform

Composite

97.5

Benchmarks tracked

217

Direct-linked

283

As of

2026-05-12

Host organisation

Marks Lab (Harvard) + OATML (Oxford) + DeepMind

Primary contacts

Debora Marks, Pascal Notin, Yarin Gal

Founded

2022

License model

MIT

Official site

GitHub

Count methodology

ProteinGym v1.2 README + NeurIPS 2023 paper: 217 DMS substitution assays + 66 indel assays + 2525 ClinVar clinical variants.

Rubric

rigor

5

coverage

5

maintenance

5

adoption

5

quality

5

accessibility

5

industry_relevance

4

Breakdown

dms_substitutions

217

dms_indels

66

mutations

2,700,000

clinical_variants

2,525

Notes

De facto standard for variant effect prediction. Clinical track enables ESM/EVE/AlphaMissense fair comparison.

Hosted benchmarks (283)

Direct-linked — each links to the benchmark’s leaderboard / detail page on the host portal.

DMS indel (66)

A4_HUMAN_Seuma_2022_indelsDMS indel AMFR_HUMAN_Tsuboyama_2023_4G3O_indelsDMS indel ARGR_ECOLI_Tsuboyama_2023_1AOY_indelsDMS indel B1LPA6_ECOSM_Russ_2020_indelsDMS indel BBC1_YEAST_Tsuboyama_2023_1TG0_indelsDMS indel BCHB_CHLTE_Tsuboyama_2023_2KRU_indelsDMS indel BLAT_ECOLX_Gonzalez_2019_indelsDMS indel CAPSD_AAV2S_Sinai_2021_designed_indelsDMS indel CAPSD_AAV2S_Sinai_2021_library_indelsDMS indel CATR_CHLRE_Tsuboyama_2023_2AMI_indelsDMS indel CBPA2_HUMAN_Tsuboyama_2023_1O6X_indelsDMS indel CBX4_HUMAN_Tsuboyama_2023_2K28_indelsDMS indel CSN4_MOUSE_Tsuboyama_2023_1UFM_indelsDMS indel CUE1_YEAST_Tsuboyama_2023_2MYX_indelsDMS indel DN7A_SACS2_Tsuboyama_2023_1JIC_indelsDMS indel DNJA1_HUMAN_Tsuboyama_2023_2LO1_indelsDMS indel DOCK1_MOUSE_Tsuboyama_2023_2M0Y_indelsDMS indel EPHB2_HUMAN_Tsuboyama_2023_1F0M_indelsDMS indel FECA_ECOLI_Tsuboyama_2023_2D1U_indelsDMS indel HCP_LAMBD_Tsuboyama_2023_2L6Q_indelsDMS indel HECD1_HUMAN_Tsuboyama_2023_3DKM_indelsDMS indel HIS7_YEAST_Pokusaeva_2019_indelsDMS indel ILF3_HUMAN_Tsuboyama_2023_2L33_indelsDMS indel KCNJ2_MOUSE_Macdonald_2022_indelsDMS indel MAFG_MOUSE_Tsuboyama_2023_1K1V_indelsDMS indel MBD11_ARATH_Tsuboyama_2023_6ACV_indelsDMS indel MYO3_YEAST_Tsuboyama_2023_2BTT_indelsDMS indel NKX31_HUMAN_Tsuboyama_2023_2L9R_indelsDMS indel NUSA_ECOLI_Tsuboyama_2023_1WCL_indelsDMS indel NUSG_MYCTU_Tsuboyama_2023_2MI6_indelsDMS indel OBSCN_HUMAN_Tsuboyama_2023_1V1C_indelsDMS indel ODP2_GEOSE_Tsuboyama_2023_1W4G_indelsDMS indel OTU7A_HUMAN_Tsuboyama_2023_2L2D_indelsDMS indel P53_HUMAN_Kotler_2018_indelsDMS indel PIN1_HUMAN_Tsuboyama_2023_1I6C_indelsDMS indel PITX2_HUMAN_Tsuboyama_2023_2L7M_indelsDMS indel PKN1_HUMAN_Tsuboyama_2023_1URF_indelsDMS indel POLG_PESV_Tsuboyama_2023_2MXD_indelsDMS indel PR40A_HUMAN_Tsuboyama_2023_1UZC_indelsDMS indel PSAE_PICP2_Tsuboyama_2023_1PSE_indelsDMS indel PTEN_HUMAN_Mighell_2018_indelsDMS indel Q8EG35_SHEON_Campbell_2022_indelsDMS indel RAD_ANTMA_Tsuboyama_2023_2CJJ_indelsDMS indel RCD1_ARATH_Tsuboyama_2023_5OAO_indelsDMS indel RD23A_HUMAN_Tsuboyama_2023_1IFY_indelsDMS indel RPC1_BP434_Tsuboyama_2023_1R69_indelsDMS indel RS15_GEOSE_Tsuboyama_2023_1A32_indelsDMS indel S22A1_HUMAN_Yee_2023_abundance_indelsDMS indel S22A1_HUMAN_Yee_2023_activity_indelsDMS indel SAV1_MOUSE_Tsuboyama_2023_2YSB_indelsDMS indel SDA_BACSU_Tsuboyama_2023_1PV0_indelsDMS indel SOX30_HUMAN_Tsuboyama_2023_7JJK_indelsDMS indel SPG2_STRSG_Tsuboyama_2023_5UBS_indelsDMS indel SPTN1_CHICK_Tsuboyama_2023_1TUD_indelsDMS indel SQSTM_MOUSE_Tsuboyama_2023_2RRU_indelsDMS indel SR43C_ARATH_Tsuboyama_2023_2N88_indelsDMS indel SRBS1_HUMAN_Tsuboyama_2023_2O2W_indelsDMS indel TCRG1_MOUSE_Tsuboyama_2023_1E0L_indelsDMS indel THO1_YEAST_Tsuboyama_2023_2WQG_indelsDMS indel TNKS2_HUMAN_Tsuboyama_2023_5JRT_indelsDMS indel UBE4B_HUMAN_Tsuboyama_2023_3L1X_indelsDMS indel UBR5_HUMAN_Tsuboyama_2023_1I2T_indelsDMS indel VG08_BPP22_Tsuboyama_2023_2GP8_indelsDMS indel VILI_CHICK_Tsuboyama_2023_1YU5_indelsDMS indel VRPI_BPT7_Tsuboyama_2023_2WNM_indelsDMS indel YNZC_BACSU_Tsuboyama_2023_2JVD_indelsDMS indel

DMS substitution (217)

A0A140D2T1_ZIKV_Sourisseau_2019DMS substitution A0A192B1T2_9HIV1_Haddox_2018DMS substitution A0A1I9GEU1_NEIME_Kennouche_2019DMS substitution A0A247D711_LISMN_Stadelmann_2021DMS substitution A0A2Z5U3Z0_9INFA_Doud_2016DMS substitution A0A2Z5U3Z0_9INFA_Wu_2014DMS substitution A4_HUMAN_Seuma_2022DMS substitution A4D664_9INFA_Soh_2019DMS substitution A4GRB6_PSEAI_Chen_2020DMS substitution AACC1_PSEAI_Dandage_2018DMS substitution ACE2_HUMAN_Chan_2020DMS substitution ADRB2_HUMAN_Jones_2020DMS substitution AICDA_HUMAN_Gajula_2014_3cyclesDMS substitution AMFR_HUMAN_Tsuboyama_2023_4G3ODMS substitution AMIE_PSEAE_Wrenbeck_2017DMS substitution ANCSZ_Hobbs_2022DMS substitution ARGR_ECOLI_Tsuboyama_2023_1AOYDMS substitution B2L11_HUMAN_Dutta_2010_binding-Mcl-1DMS substitution BBC1_YEAST_Tsuboyama_2023_1TG0DMS substitution BCHB_CHLTE_Tsuboyama_2023_2KRUDMS substitution BLAT_ECOLX_Deng_2012DMS substitution BLAT_ECOLX_Firnberg_2014DMS substitution BLAT_ECOLX_Jacquier_2013DMS substitution BLAT_ECOLX_Stiffler_2015DMS substitution BRCA1_HUMAN_Findlay_2018DMS substitution BRCA2_HUMAN_Erwood_2022_HEK293TDMS substitution C6KNH7_9INFA_Lee_2018DMS substitution CALM1_HUMAN_Weile_2017DMS substitution CAPSD_AAV2S_Sinai_2021DMS substitution CAR11_HUMAN_Meitlis_2020_gofDMS substitution CAR11_HUMAN_Meitlis_2020_lofDMS substitution CAS9_STRP1_Spencer_2017_positiveDMS substitution CASP3_HUMAN_Roychowdhury_2020DMS substitution CASP7_HUMAN_Roychowdhury_2020DMS substitution CATR_CHLRE_Tsuboyama_2023_2AMIDMS substitution CBPA2_HUMAN_Tsuboyama_2023_1O6XDMS substitution CBS_HUMAN_Sun_2020DMS substitution CBX4_HUMAN_Tsuboyama_2023_2K28DMS substitution CCDB_ECOLI_Adkar_2012DMS substitution CCDB_ECOLI_Tripathi_2016DMS substitution CCR5_HUMAN_Gill_2023DMS substitution CD19_HUMAN_Klesmith_2019_FMC_singlesDMS substitution CP2C9_HUMAN_Amorosi_2021_abundanceDMS substitution CP2C9_HUMAN_Amorosi_2021_activityDMS substitution CSN4_MOUSE_Tsuboyama_2023_1UFMDMS substitution CUE1_YEAST_Tsuboyama_2023_2MYXDMS substitution D7PM05_CLYGR_Somermeyer_2022DMS substitution DLG4_HUMAN_Faure_2021DMS substitution DLG4_RAT_McLaughlin_2012DMS substitution DN7A_SACS2_Tsuboyama_2023_1JICDMS substitution DNJA1_HUMAN_Tsuboyama_2023_2LO1DMS substitution DOCK1_MOUSE_Tsuboyama_2023_2M0YDMS substitution DYR_ECOLI_Nguyen_2023DMS substitution DYR_ECOLI_Thompson_2019DMS substitution ENV_HV1B9_DuenasDecamp_2016DMS substitution ENV_HV1BR_Haddox_2016DMS substitution ENVZ_ECOLI_Ghose_2023DMS substitution EPHB2_HUMAN_Tsuboyama_2023_1F0MDMS substitution ERBB2_HUMAN_Elazar_2016DMS substitution ESTA_BACSU_Nutschel_2020DMS substitution F7YBW8_MESOW_Ding_2023DMS substitution F7YBW8_MESOW_Aakre_2015DMS substitution FECA_ECOLI_Tsuboyama_2023_2D1UDMS substitution FKBP3_HUMAN_Tsuboyama_2023_2KFVDMS substitution GAL4_YEAST_Kitzman_2015DMS substitution GCN4_YEAST_Staller_2018DMS substitution GDIA_HUMAN_Silverstein_2021DMS substitution GFP_AEQVI_Sarkisyan_2016DMS substitution GLPA_HUMAN_Elazar_2016DMS substitution GRB2_HUMAN_Faure_2021DMS substitution HCP_LAMBD_Tsuboyama_2023_2L6QDMS substitution HECD1_HUMAN_Tsuboyama_2023_3DKMDMS substitution HEM3_HUMAN_Loggerenberg_2023DMS substitution HIS7_YEAST_Pokusaeva_2019DMS substitution HMDH_HUMAN_Jiang_2019DMS substitution HSP82_YEAST_Cote-Hammarlof_2020_growth-H2O2DMS substitution HSP82_YEAST_Flynn_2019DMS substitution HSP82_YEAST_Mishra_2016DMS substitution HXK4_HUMAN_Gersing_2022_activityDMS substitution HXK4_HUMAN_Gersing_2023_abundanceDMS substitution I6TAH8_I68A0_Doud_2015DMS substitution IF1_ECOLI_Kelsic_2016DMS substitution ILF3_HUMAN_Tsuboyama_2023_2L33DMS substitution ISDH_STAAW_Tsuboyama_2023_2LHRDMS substitution KCNE1_HUMAN_Muhammad_2023_expressionDMS substitution KCNE1_HUMAN_Muhammad_2023_functionDMS substitution KCNH2_HUMAN_Kozek_2020DMS substitution KCNJ2_MOUSE_Coyote-Maestas_2022_functionDMS substitution KCNJ2_MOUSE_Coyote-Maestas_2022_surfaceDMS substitution KKA2_KLEPN_Melnikov_2014DMS substitution LGK_LIPST_Klesmith_2015DMS substitution LYAM1_HUMAN_Elazar_2016DMS substitution MAFG_MOUSE_Tsuboyama_2023_1K1VDMS substitution MBD11_ARATH_Tsuboyama_2023_6ACVDMS substitution MET_HUMAN_Estevam_2023DMS substitution MK01_HUMAN_Brenan_2016DMS substitution MLAC_ECOLI_MacRae_2023DMS substitution MSH2_HUMAN_Jia_2020DMS substitution MTH3_HAEAE_RockahShmuel_2015DMS substitution MTHR_HUMAN_Weile_2021DMS substitution MYO3_YEAST_Tsuboyama_2023_2BTTDMS substitution NCAP_I34A1_Doud_2015DMS substitution NKX31_HUMAN_Tsuboyama_2023_2L9RDMS substitution NPC1_HUMAN_Erwood_2022_HEK293TDMS substitution NPC1_HUMAN_Erwood_2022_RPE1DMS substitution NRAM_I33A0_Jiang_2016DMS substitution NUD15_HUMAN_Suiter_2020DMS substitution NUSA_ECOLI_Tsuboyama_2023_1WCLDMS substitution NUSG_MYCTU_Tsuboyama_2023_2MI6DMS substitution OBSCN_HUMAN_Tsuboyama_2023_1V1CDMS substitution ODP2_GEOSE_Tsuboyama_2023_1W4GDMS substitution OPSD_HUMAN_Wan_2019DMS substitution OTC_HUMAN_Lo_2023DMS substitution OTU7A_HUMAN_Tsuboyama_2023_2L2DDMS substitution OXDA_RHOTO_Vanella_2023_activityDMS substitution OXDA_RHOTO_Vanella_2023_expressionDMS substitution P53_HUMAN_Giacomelli_2018_Null_EtoposideDMS substitution P53_HUMAN_Giacomelli_2018_Null_NutlinDMS substitution P53_HUMAN_Giacomelli_2018_WT_NutlinDMS substitution P53_HUMAN_Kotler_2018DMS substitution P84126_THETH_Chan_2017DMS substitution PA_I34A1_Wu_2015DMS substitution PABP_YEAST_Melamed_2013DMS substitution PAI1_HUMAN_Huttinger_2021DMS substitution PHOT_CHLRE_Chen_2023DMS substitution PIN1_HUMAN_Tsuboyama_2023_1I6CDMS substitution PITX2_HUMAN_Tsuboyama_2023_2L7MDMS substitution PKN1_HUMAN_Tsuboyama_2023_1URFDMS substitution POLG_CXB3N_Mattenberger_2021DMS substitution POLG_DEN26_Suphatrakul_2023DMS substitution POLG_HCVJF_Qi_2014DMS substitution POLG_PESV_Tsuboyama_2023_2MXDDMS substitution PPARG_HUMAN_Majithia_2016DMS substitution PPM1D_HUMAN_Miller_2022DMS substitution PR40A_HUMAN_Tsuboyama_2023_1UZCDMS substitution PRKN_HUMAN_Clausen_2023DMS substitution PSAE_PICP2_Tsuboyama_2023_1PSEDMS substitution PTEN_HUMAN_Matreyek_2021DMS substitution PTEN_HUMAN_Mighell_2018DMS substitution Q2N0S5_9HIV1_Haddox_2018DMS substitution Q53Z42_HUMAN_McShan_2019_binding-TAPBPRDMS substitution Q53Z42_HUMAN_McShan_2019_expressionDMS substitution Q59976_STRSQ_Romero_2015DMS substitution Q6WV12_9MAXI_Somermeyer_2022DMS substitution Q837P4_ENTFA_Meier_2023DMS substitution Q837P5_ENTFA_Meier_2023DMS substitution Q8WTC7_9CNID_Somermeyer_2022DMS substitution R1AB_SARS2_Flynn_2022DMS substitution RAD_ANTMA_Tsuboyama_2023_2CJJDMS substitution RAF1_HUMAN_Zinkus-Boltz_2019DMS substitution RASH_HUMAN_Bandaru_2017DMS substitution RASK_HUMAN_Weng_2022_abundanceDMS substitution RASK_HUMAN_Weng_2022_binding-DARPin_K55DMS substitution RBP1_HUMAN_Tsuboyama_2023_2KWHDMS substitution RCD1_ARATH_Tsuboyama_2023_5OAODMS substitution RCRO_LAMBD_Tsuboyama_2023_1ORCDMS substitution RD23A_HUMAN_Tsuboyama_2023_1IFYDMS substitution RDRP_I33A0_Li_2023DMS substitution REV_HV1H2_Fernandes_2016DMS substitution RFAH_ECOLI_Tsuboyama_2023_2LCLDMS substitution RL20_AQUAE_Tsuboyama_2023_1GYZDMS substitution RL40A_YEAST_Mavor_2016DMS substitution RL40A_YEAST_Roscoe_2013DMS substitution RL40A_YEAST_Roscoe_2014DMS substitution RNC_ECOLI_Weeks_2023DMS substitution RPC1_BP434_Tsuboyama_2023_1R69DMS substitution RPC1_LAMBD_Li_2019_high-expressionDMS substitution RPC1_LAMBD_Li_2019_low-expressionDMS substitution RS15_GEOSE_Tsuboyama_2023_1A32DMS substitution S22A1_HUMAN_Yee_2023_abundanceDMS substitution S22A1_HUMAN_Yee_2023_activityDMS substitution SAV1_MOUSE_Tsuboyama_2023_2YSBDMS substitution SBI_STAAM_Tsuboyama_2023_2JVGDMS substitution SC6A4_HUMAN_Young_2021DMS substitution SCIN_STAAR_Tsuboyama_2023_2QFFDMS substitution SCN5A_HUMAN_Glazer_2019DMS substitution SDA_BACSU_Tsuboyama_2023_1PV0DMS substitution SERC_HUMAN_Xie_2023DMS substitution SHOC2_HUMAN_Kwon_2022DMS substitution SOX30_HUMAN_Tsuboyama_2023_7JJKDMS substitution SPA_STAAU_Tsuboyama_2023_1LP1DMS substitution SPG1_STRSG_Olson_2014DMS substitution SPG1_STRSG_Wu_2016DMS substitution SPG2_STRSG_Tsuboyama_2023_5UBSDMS substitution SPIKE_SARS2_Starr_2020_bindingDMS substitution SPIKE_SARS2_Starr_2020_expressionDMS substitution SPTN1_CHICK_Tsuboyama_2023_1TUDDMS substitution SQSTM_MOUSE_Tsuboyama_2023_2RRUDMS substitution SR43C_ARATH_Tsuboyama_2023_2N88DMS substitution SRBS1_HUMAN_Tsuboyama_2023_2O2WDMS substitution SRC_HUMAN_Ahler_2019DMS substitution SRC_HUMAN_Chakraborty_2023_binding-DAS_25uMDMS substitution SRC_HUMAN_Nguyen_2022DMS substitution SUMO1_HUMAN_Weile_2017DMS substitution SYUA_HUMAN_Newberry_2020DMS substitution TADBP_HUMAN_Bolognesi_2019DMS substitution TAT_HV1BR_Fernandes_2016DMS substitution TCRG1_MOUSE_Tsuboyama_2023_1E0LDMS substitution THO1_YEAST_Tsuboyama_2023_2WQGDMS substitution TNKS2_HUMAN_Tsuboyama_2023_5JRTDMS substitution TPK1_HUMAN_Weile_2017DMS substitution TPMT_HUMAN_Matreyek_2018DMS substitution TPOR_HUMAN_Bridgford_2020DMS substitution TRPC_SACS2_Chan_2017DMS substitution TRPC_THEMA_Chan_2017DMS substitution UBC9_HUMAN_Weile_2017DMS substitution UBE4B_HUMAN_Tsuboyama_2023_3L1XDMS substitution UBE4B_MOUSE_Starita_2013DMS substitution UBR5_HUMAN_Tsuboyama_2023_1I2TDMS substitution VG08_BPP22_Tsuboyama_2023_2GP8DMS substitution VILI_CHICK_Tsuboyama_2023_1YU5DMS substitution VKOR1_HUMAN_Chiasson_2020_abundanceDMS substitution VKOR1_HUMAN_Chiasson_2020_activityDMS substitution VRPI_BPT7_Tsuboyama_2023_2WNMDMS substitution YAIA_ECOLI_Tsuboyama_2023_2KVTDMS substitution YAP1_HUMAN_Araya_2012DMS substitution YNZC_BACSU_Tsuboyama_2023_2JVDDMS substitution

← Back to all initiatives

Compare:

Open comparison →