SARS-CoV-2 sequence models 3D contact predictions & in silico mutation scans

protein NCBI sequence UniProt sequence model
(full .zip)
# aligned sequences (N) effective # sequences (Neff) cluster identity threshold (theta) evolutionary couplings in silico mutation scans complete natural sequence model multiple sequence alignment description
Nsp1 YP_009725297 R1AB_SARS2 nsp1 1434 111.1 0.99 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp2 YP_009725298 R1AB_SARS2 nsp2 1-260 2462 426.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp2 YP_009725298 R1AB_SARS2 nsp2 400-638 2339 511.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 1-560 254 88.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 97-174 6271 1587.0 0.8 download download download download Virus alignment. TBD
Nsp3 YP_009725299 R1AB_SARS2 nsp3 235-680 2637 699.0 0.8 download download download download Virus alignment. Structure prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 408-680 19426 5216.7 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 560-1206 1418 341.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 1200-1945 3061 1051.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp3 YP_009725299 R1AB_SARS2 nsp3 1550-1945 140813 32622.9 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp4 YP_009725300 R1AB_SARS2 nsp4 3087 939.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp5 YP_009725301 R1AB_SARS2 nsp5 110-220 3169 26.6 0.8 download download download download Virus alignment. TBD
Nsp5 YP_009725301 R1AB_SARS2 nsp5 deeper 33095 7567.4 0.8 download download download download Virus & cellular alignment. TBD
Nsp5 YP_009725301 R1AB_SARS2 nsp5 3106 718.0 0.999 download download download download Virus alignment. Structure prediction
Nsp6 YP_009725302 R1AB_SARS2 nsp6 3111 725.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp6 YP_009725302 R1AB_SARS2 nsp6 deeper 11814 2971.7 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp7 YP_009725303 R1AB_SARS2 nsp7 1-83 3162 51.5 0.9 download download download download Virus alignment. SARS-CoV-2 mutant effect & structure prediction
Nsp8 YP_009725304 R1AB_SARS2 nsp8 3124 457.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp9 YP_009725305 R1AB_SARS2 nsp9 3203 348.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp10 YP_009725306 R1AB_SARS2 nsp10 3138 390.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp11 None None nsp11 1366 136.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp12 YP_009725307 R1AB_SARS2 nsp12 500-932 23925 2072.6 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp13 YP_009725308 R1AB_SARS2 nsp13 153-601 40851 11001.1 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp14 YP_009725309 R1AB_SARS2 nsp14 2268 828.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nsp15 YP_009725310 R1AB_SARS2 nsp15 189-346 5119 560.2 0.8 download download download download Virus & cellular alignment. Structure prediction
Nsp15 YP_009725310 R1AB_SARS2 nsp15 2294 829.0 0.999 download download download download Virus alignment. SARS-CoV-@ mutant effect prediction
Nsp16 YP_009725311 R1AB_SARS2 nsp16 2335 671.0 0.999 download download download download Virus alignment. SARS-CoV-@ mutant effect prediction
Nsp16 YP_009725311 R1AB_SARS2 nsp16 deeper 68190 52324.5 0.999 download download download download Virus & cellular alignment. Structure prediction
Spike YP_009724390 SPIKE_SARS2 spike 3168 2722.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Membrane YP_009724393 VME1_SARS2 membrane 1743 1218.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Envelope YP_009724392 VEMP_SARS2 envelope 658 335.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction
Nucleocapsid YP_009724397 NCAP_SARS2 nucleocapsid 1805 1421.0 0.999 download download download download Virus alignment. SARS-CoV-2 mutant effect prediction


Contact: sarscov2@hms.harvard.edu | Lab websites: Marks lab. Sander lab.