PPI Prediction Challenge 1
We have a challenge for anyone who claims they can predict protein-protein interactions.
Here is binding data: 15 novel binders, each bind one of 15 target proteins selectively (with some LC3B/GABARAP crosstalk, expected due to similarity). This is real data.
now next, lets see what alphafold3 predicts should bind within this 15x15 potential array of PPIs...
So, if you or someone you know thinks they can actually predict PPIs, prove it. Here is a link to our blinded sequence data:
Here are 18 engineered mini-protein binders:
GSVKVKFIFSGEEKEVDTSKIHAVFRNGKYVTFFYDDNGKHGFGSVLEKDAPKELLDMLARAEREKKL
GSVKVKFSHAGEEKEVDTSKIRIVCRAGKLVYFLYDDNGKRGCGLVYEKDAPKELLDMLARAEREKKL
GSVKVKFVVRGEEKEVDTSKIRSVWRGGKWVDFSYDDNGKQGYGYVLEKDAPKELLDMLARAEREKKL
VDNKFNKEGDTAVLEIGHLPNLNLHQQYAFLHSLYNDPSQSANLLAEAKKLNDAQAPK
VDNKFNKELFYAFHQIYALPNLNAAQVRAFVGSLDDDPSQSANLLAEAKKLNDAQAPK
VDNKFNKEPRAARLEITVLPNLNREQGGAFIVSLWDDPSQSANLLAEAKKLNDAQAPK
VDNKFSKEVFTAFDQIGGLPNLNLCQKDAFICSLVDDPSQSANLLAEAKKLNDAQAPK
VDNKFSKEVGAADGEIVGLPNLNGSQKIAFLRSLVNDPSQSANLLAEAKKLNDAQAPK
VDNKFSKEWIDAFVEINFLPNLNRNQRCAFVNSLLNDPSQSANLLAEAKKLNDAQAPK
VDNKFSKEWSDAVYEIGRLPNLNGYQGGAFINSLVNDPSQSANLLAEAKKLNDAQAPK
VDNKFTKEVDDASFEILYLPNLNDFQENAFLVSLSDDPSQSANLLAEAKKLNDAQAPK
VDNKFTKEVDSAVFEIHILPNLNDYQRVAFIFSLFDDPSQSANLLAEAKKLNDAQAPK
VDNKFYKEVDAAASEICSLPNLNRNQRSAFICSLYNDPSQSANLLAEAKKLNDAQAPK
VKVKFFDAGEEKEVDTSKIFPVPRYGKYVIFYYDDNGKVGRGSVNEKDAPKELLDMLARAEREKKL
VKVKFRRPGEEKEVDTSKIGYVHRVGKFVAFFYDDNGKIGSGTVSEKDAPKELLDMLARAEREKKL
VKVKFSSAGEEKEVDTSKIFVVRRLGKYVGFTYDDNGKAGLGLVCEKDAPKELLDMLARAEREKKL
VKVKFSYAGEEKEVDTSKIYHVSRLGKDVIFCYDDNGKVGSGAVFEKDAPKELLDMLARAEREKKL
VKVKFTDCGEEKEVDTSKITYVIRFGKFVDFDYDDNGKIGSGAVREKDAPKELLDMLARAEREKKL
16 of which, bind one each of these 16 targets:
1 MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSSHLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDS
2 MDISNPETIRRASSSMSVNVLKGDAIKNYALSEKQYIPFFGSSELSRISPFHPSVLAEKYQRNYRPFLLGAPGTQSLSQYMMMRSAGDAMKNKKVVFIISPQWFVKNGVKTDYFNTYYSELQTYDWLFSMKKVTPADRYLARRLLTFSKVKENDTLTAILQTIKKGKLPLPESLNQLRSQWNMLKREDEVFSNIGLKDRQQKIDHESKRLPKQYQETELSILANQIGERETTNNPFGLKNDFYTHRIRAHEPELKQSQKNWDYRFSPEFSDFQLVLDQLAKNHNEVLFIIPPVNEKWSDYTGLSQEMLQGFAKKIKFQLNSQGFNRIADFVNQAGTNYFMEDTIHLGWKGWLAADQQIRPFLEENHITASKYHLDDAFFSKSWQHQIPDKLQLK
3 MDKNELVQKAKQAEQAEDYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSEWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN
4 MDKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQGEHP
5 MDYYKVKDNSIRYSTSYEKYKSRDILTSNITPNTLVLMGSSELVATINEDYHPNKIFNYNDFNIMQIGTSYSQNIIQATTLGSIEGSMTKRKVAIVESVQWFEKDGTHQDAFLNKASQEHIFHMLDNGKISKETKEKLINRIIEITKGNKQQNDIYKKYKSYFIDGKGTIVDKKLLEFENAMYSFKLKQTFYQKHAKSDYPSLGDKTPDYDWQKMTNQFVEEVKQKTDNNDYAVDNNYYNTYLKDRYASLKDSNKDLSYLESPEYSDMELFLTVAKELGIEVEVIIFPVNGKWNDYTGVSREMREKTYKKIEDVAKSHGATVLNYGNREYDDYFLFDVMHVGVKGWMEVEKELYKFANQAN
6 MEGAGGANDKKKISSERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASVMRLTISYLRVRKLLDAGDLDIEDDMKAQMNCFYLKALDGFVMVLTDDGDMIYISDNVNKYMGLTQFELTGHSVFDFTHPCDHEEMREMLTHRNGLVKKGKEQNTQRSFFLRMKCTLTSRGRTMNIKSATWKVLHCTGHIHVYDTNSNQPQCGYKKPPMTCLVLICEPIPHPSNIEIPLDSKTFLSRHSLDMKFSYCDERITELMGYEPEELLGRSIYEYYHALDSDHLTKTHHDMFTKGQVTTGQYRMLAKRGGYVWVETQATVIYNTKNSQPQCIVCVNYVVSGIIQHDL
7 MGNIGSLSTIPTAAPPSSTGVRKGWHEHVTQDLRSHLVHKLVQAIFPTPDPAALKDRRMENLVAYAKKVEGDMYESANSRDEYYHLLAEKIYKIQKELEEKRRSRL
8 MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
9 MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
10 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL
11 MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFGMKLSV
12 MQDPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKEESDRKIMQSQIVSFYFKLFKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDDFEKLTNYSVTDLNVQRKAIHELIQVMAELSPAAKTGKRKRSQ
13 MSKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFL
14 MTCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTWASHEKMHEGDEGPGHHHKPGLGEGTPGGSGGSGGSGGSMLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEESHKE
15 MTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM
16 MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK