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.
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now next, lets see what alphafold3 predicts should bind within this 15x15 potential array of PPIs...
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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