Protein structure analysis workflow

Installation

The following commands install dependencies of the workflow in the current directory within the .pixi folder. After installation, you cannot move the folder without re-installling all the dependencies.

curl -fsSL https://pixi.sh/install.sh | bash
# ... cd <this repo>
pixi install

Because of the dependency on apptainer, this workflow only works on linux. Pixi installs all the requirements: conda, pymol and snakemake. Snakemake takes care of the rest.

Usage

Run pixi run help for the help page. Targets can be made using pixi run make <target>

Place your own structures in the data directory. You can supply zip files that contain your structures, the pipeline will automatically unpack them. If a analysis is requested on a structure that cannot be found in data, an attempt is made to download it from the pdb.

Example

Alignment between 2 V atpases

In this example, we will compare the structures of yeast V-ATPase state 2 (6O7W) to that of Citrus (7UWB)

In the terminal type

# takes 20 mins to complete.
pixi run make results/contact-map/6o7v results/contact-map/7uwb results/comparison/7uwb-6o7w.tmscore.txt results/plip/6o7v results/plip/7uwb results/comparison/7uwb-6o7w.usalign.txt results/comparison/7uwb-6o7w.usalign.sup.png  results/comparison/7uwb-6o7w.usalign.sup.pse  --cores 5

To start the analysis with 5 paralel processes. This will download the structures and the programmes, and run the analysis.

Subunit interaction graph between 6o7v (left) and 7uwb (right)

 ********************************************************************
 * US-align (Version 20231222)                                      *
 * Universal Structure Alignment of Proteins and Nucleic Acids      *
 * Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Nat Methods*
 * Please email comments and suggestions to zhang@zhanggroup.org    *
 ********************************************************************

Name of Structure_1: results/input/7uwb.pdb:1,A:1,B:1,C:1,D:1,E:1,F:1,G:1,H:1,I:1,J:1,K:1,L:1,M:1,N:1,O:1,P:1,a:1,b:1,c:1,d:1,e:1,g:1,h:1,i:1,j:1,k:1,l:1,m:1,n:1,r:1,o: (to be superimposed onto Structure_2)
Name of Structure_2: results/input/6o7w.pdb:1,C:1,D:1,E:1,F:1,A:1,B:1,G:1,H:1,I:1,J:1,K:1,L:1,M:1,N:1,O:1,P:1,a:1,b:1,c:1,d:1,e:1,g:1,h:1,i:1,k:1,l:1,m:1,n:1,o:1,j::1,f
Length of Structure_1: 7683 residues
Length of Structure_2: 8038 residues

Aligned length= 7339, RMSD=   5.26, Seq_ID=n_identical/n_aligned= 0.495
TM-score= 0.91077 (normalized by length of Structure_1: L=7683, d0=22.65)
TM-score= 0.87174 (normalized by length of Structure_2: L=8038, d0=23.02)
(You should use TM-score normalized by length of the reference structure)

(":" denotes residue pairs of d < 5.0 Angstrom, "." denotes other aligned residues)
YGYVRKVSGPVVIADGMNGAAMYELVRVGHDNLIGEIIRLEGDSATIQVYEETAGLMVNDPVLRTHKPLSVELGPGILGNIFDGIQRPLKTIAIRSGDVYIPRGVSVPALDKDTLWEFQPKKIGEGDLLTGGDLYATVFENSLM-QHHVALPPDAMGKVTYVAPAGQYSLKDTVLELEFQGVKKSFTMLQAWPVRTPRPVSSKLAADTPLLTGQRVLDALFPSVLGGTCAIPGAFGCGKTVISQALSKYSNSDTVVYVGCGERGNEMAEVLMDFPQLTMTLPDGREESVMKRTTLVANTSNMPVAAREASIYTGITIAEYFRDMGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLAARLASFYERAGKVKCLGGPERTGSVTIVGAVSPPGGDFSDPVTSATLSIVQVFWGLDKKLAQRKHFPSVNWLISYSKYSTALESFYEQFDPDFINIRTKAREVLQREDDLNEIVQLVGKDALAEGDKITLETAKLLREDYLAQNAFTPYDKFCPFYKSVWMMRNIIHFYNLANQAV---ITYTLIKHRLGDLFYRLVSQKFEDPAEGEPALVAKFKKLHEDLTAGFRALE-*LEVAMEYRTVTGVAGPLVILDKVKGPKYYEIVNIRLGDGTMRRGQVLEVDGEKAVVQVFEGTSGIDNKFTTVQFTGEVLKTPVSLDMLGRIFNGSGKPIDNGPPILPEAYLDISGSSINPSERTYPEEMIQTGISTIDVMNSIARGQKIPLFSAAGLPHNEIAAQICRQAG--L-VKRLEK---DNFAIVFAAMGVNMETAQFFKRDFEENGSMERVTLFLNLANDPTIERIITPRIALTTAEYLAYECGKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLAQIYERAGRIEGRKGSITQIPILTMPNDDITHPTPDLTGYITEGQIYIDRQLQNRQIYPPINVLPSLSRLMKSAIGEGMTRRDHSDVSNQLYANYAIGKDVQAMKAVVGEEALSSEDLLYLEFLDKFERKFVAQGAYDSRNIFQSLDLAWTLLRIFPRELLHRIPGKTLDQYYSR*YGYVRKVSGPVVIADGMNGAAMYELVRVGHDNLIGEIIRLEGDSATIQVYEETAGLMVNDPVLRTHKPLSVELGPGILGNIFDGIQRPLKTIAIRSGDVYIPRGVSVPALDKDTLWEFQPKKIGEGDLLTGGDLYATVFENSL-MQHHVALPPDAMGKVTYVAPAGQYSLKDTVLELEFQGVKKSFTMLQAWPVRTPRPVSSKLAADTPLLTGQRVLDALFPSVLGGTCAIPGAFGCGKTVISQALSKYSNSDTVVYVGCGERGNEMAEVLMDFPQLTMTLPDGREESVMKRTTLVANTSNMPVAAREASIYTGITIAEYFRDMGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLAARLASFYERAGKVKCLGGPERTGSVTIVGAVSPPGGDFSDPVTSATLSIVQVFWGLDKKLAQRKHFPSVNWLISYSKYSTALESFYEQFDPDFINIRTKAREVLQREDDLNEIVQLVGKDALAEGDKITLETAKLLREDYLAQNAFTPYDKFCPFYKSVWMMRNIIHFYNLANQAVEKGAGMDGQKITYTLIKHRLGDLFYRLVSQKFEDPAEGEPALVAKFKKLHEDLTAGFRALEDETR*EGTLEVAMEYRTVTGVAGPLVILDKVKGPKYYEIVNIRLGDGTMRRGQVLEVDGEKAVVQVFEGTSGIDNKFTTVQFTGEVLKTPVSLDMLGRIFNGSGKPIDNGPPILPEAYLDISGSSINPSERTYPEEMIQTGISTIDVMNSIARGQKIPLFSAAGLPHNEIAAQICRQA--GLVKRLEKDGEEDNFAIVFAAMGVNMETAQFFKRDFEENGSMERVTLFLNLANDPTIERIITPRIALTTAEYLAYECGKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLAQIYERAGRIEGRKGSITQIPILTMPNDDITHPTPDLTGYITEGQIYIDRQLQNRQIYPPINVLPSLSRLMKSAIGEGMTRRDHSDVSNQLYANYAIGKDVQAMKAVVGEEALSSEDLLYLEFLDKFERKFVAQGAYDSRNIFQSLDLAWTLLRIFPRELLHRIPGKTLDQYYSR*YGYVRKVSGPVVIADGMNGAAMYELVRVGHDNLIGEIIRLEGDSATIQVYEETAGLMVNDPVLRTHKPLSVELGPGILGNIFDGIQRPLKTIAIRSGDVYIPRGVSVPALDKDTLWEFQPKKIGEGDLLTGGDLYATVFENSLMQH-HVALPPDAMGKVTYVAPAGQYSLKDTVLELEFQGVKKSFTMLQAWPVRTPRPVSSKLAADTPLLTGQRVLDALFPSVLGGTCAIPGAFGCGKTVISQALSKYSNSDTVVYVGCGERGNEMAEVLMDFPQLTMTLPDGREESVMKRTTLVANTSNMPVAAREASIYTGITIAEYFRDMGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLAARLASFYERAGKVKCLGGPERTGSVTIVGAVSPPGGDFSDPVTSATLSIVQVFWGLDKKLAQRKHFPSVNWLISYSKYSTALESFYEQFDPDFINIRTKAREVLQREDDLNEIVQLVGKDALAEGDKITLETAKLLREDYLAQNAFTPYDKFCPFYKSVWMMRNIIHFYNLANQAVEKGAGMDGQKITYTLIKHRLGDLFYRLVSQKFEDPAEGEPALVAKFKKLHEDLTAGFRALEDETR*EGTLEVAMEYRTVTGVAGPLVILDKVKGPKYYEIVNIRLGDGTMRRGQVLEVDGEKAVVQVFEGTSGIDNKFTTVQFTGEVLKTPVSLDMLGRIFNGSGKPIDNGPPILPEAYLDISGSSINPSERTYPEEMIQTGISTIDVMNSIARGQKIPLFSAAGLPHNEIAAQICRQA--GL--V-KRG-EEDNFAIVFAAMGVNMETAQFFKRDFEENGSMERVTLFLNLANDPTIERIITPRIALTTAEYLAYECGKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLAQIYERAGRIEGRKGSITQIPILTMPNDDITHPTPDLTGYITEGQIYIDRQLQNRQIYPPINVLPSLSRLMKSAIGEGMTRRDHSDVSNQLYANYAIGKDVQAMKAVVGEEALSSEDLLYLEFLDKFERKFVAQGAYDSRNIFQSLDLAWTLLRIFPRELLHRIPGKTLDQYYSR*----------Q-MVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIRKKIEYSMQLNASRIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQ-VHPPEIIV-HHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVS*---------LAAEQEAQHIVAAARNAKMARLRQAKEEAEREIAEHRAQVEREFQRKLAESSGDSGANVKRLEQETEVKIHHLNAGAEKIQYDVVQMLLKHVTTVKN*-----------MV-RFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIRKKIEYSMQLNASRIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEILPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVS*-----L-AAEQEAQHIVAAARNAKMARLRQAKEEAEREIAEHRAQVEREFQRKLAESSGDSGANVKRLEQETEVKIHHLNAGAEKIQYDVVQMLLKH-VT-TVK-*-NDADVSKQIQQMVRFIRQEAEEKANEISVSAEEEFNIEKLQLVEAEKKKIRQEYERKEKQVEIRKKIEYSMQLNASRIKVLQAQDDLVSNMMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVS*----GIQQLLAAEQEAQHIVAAARNAKMARLRQAKEEAEREIAEHRAQVEREFQRKLAESSGDSGANVKRLEQETEVKIHHLNAGAEKIQYDVVQMLLKHVTTVK*VVPTVTMLGVMKSRLVGATRGHALLKKKSDALTVQFRQILKNIVTTKESMGEVMKDSSFALIEAKYVAGENIKHIVLENVQNASIKVRSRQENIAGVKIPKFEYFTDGETKNDLTG-----LARGGQQVQQCRAAYVKAIELLVELASLQTSFLTLDEAIKTTNRRVNALENVVKPRLENTITYIKGELDELEREDFFRLKKIQGYKKREIERQLASS*---SALIAMIADEDTVTGFLLAGVGNVDL-RRKTNYLIVDS-KTTVKAIEDAFKEFT-TKEDIAIVLISQYVANMIRFLVDSYNKPIPAILEIPSKDHPYDPAHDSVLSRVKN--*--ASR----YWVVSLPV--QNSAAS--VWNRLQEQISKHSFDTPLYRFNIPNLRVGTLDSLLALSDDLVKSNSFVESVSHKIRRQIEELERVSGIESSSLSVDGVPVDTYLTRFVWDEAKYPTMSPLREIVDGIHTLVAKIEDDLKVRVAEYNNVRSQLNAINRKQSGSLAVRDLS-NL---VK------LVTLLAVV---P--------TS--YVVPRSSKLLYED----LYTVTLFGRVAD-NFRIAAREKGFQIRDFEYSSEAQESRNQELEKLVHDQESLRSSLLQWCYTSYGEVFSSWMHFCAVRVFAESILRYGL-P-PSFLACVL-APSVKGEKKV-RSILEE------LC----------------------G-----------*------DH---AELTTEQVLK--RDIPL--Q----LLRRYDNRSESHRAQLLDDDGPSYVRVFVSILRDIYKEETVEYVLALIDEMKR-A--RLFHDKSLASEDTYEPFLRLLWKGN-W-FIQEKSCKILASIVSARIDDVLKLLVEWLCA-QLKKP-S-HPSRGVPVAINCLAALLKEPMVRSSFVQADG-VKLLTP-LISPA-----------ST-Q-QSIQLLYETCLCVWLLSYYEPAVEYLATTR--TLPRLIDVVKSSTKEKVVRVVVLILRNLLP--K--G-NFAAQMID-LGLPQVVQSLKAQAWSDEDLLEGLNQLEEGLKDNI--------------------------------------------------------------------------------------------------------------------------------*PMQLVQIIIPIESAHLTVSYLGELGLLQFKDLNSEKSPFQRTYAAQIKKCAEMARKLRFFKEQMLKAGIL---SDLEVKLGDLEAELVEINANGDKLQRAHSELVEYKLVLQKAGEFFSSALTSAAAQQKLGFIAGLVPREKSMSFERMLFRATRGNVFLRQAVVDEPVVDPVSGEKMEKNVFVVFYSGERAKNKILKICDAFGANRYPFNEEFDKQAQAISEVSGRLSELKTTLDAGLLHRGNLLQTIGDQFEQWNLLVKREKSIYHTLNMLSLDVTKKCLVGEGWSPVFATKQIQDALERAAFDSNSQVGAIFQVLHTKESPPTYFRTNKFTSAFQEIVDAYGVAKYREANPGVFTIVTFPFLFAVMFGDWGHGICLLLGTLVLIVREKKLASQKLDDITDMTFGGRYVILMMALFSIYTGLIYNEFFSVPFEIFSHSAYACRDLSCSEATTVGLIKVRDTYPFGVDPVWHGSRSELPFLNSLKMKMSILLGVAQMNLGIILSYFNATFFRIGVNIWCQFIPQIIFLNSLFGYLSLLIILKWITGSQA--DLYHVMIYMFLSP--TDELGDNQLFPGQKTAQLVLLLLAFVSVPWMLLPKPFILKMQH---------HQMIHTIEFVLGAVSNTASYLRLWALSLAHSELSSVFYE-KVLLLAW-GYNNILILIVGIIVFIFATVGVLLVMETLSAFLHALRLHWVEFQNKFYEGDGYKFSPFSFALLD*XXXX-XXXXXXXXXXXXXXXXXXXX-XXXXXXXX----------*---------------------------S-SWSRALVKISPYTFSAIGIAVAIGVSVLGAAWGIYITGSSLIGAAIKAPRITSKNLISVIFCEAVAIYGVIVAIILQTKLESVPASQIYAPESLRAGYAIFASGIIVGFANLVCGLCVGIIGSSCALSDAQNSSLFVKILVIEIFGSALGLFGVIVGII-MSAQASWP*AMTFNIHGGYLEAIVRGYR-A--------------------------GLL--------------TIVEKCTLKLVDEYKH-ML----PLSTFLEYITYGHMIDNVVLIVT--GRDVQ--ELLEKCHPLGMFDSI-------MRELYRL-VLVDTPLAPYFSECITS-EDLDDMNIEIMRNTLYKAYLEDFYKFCQ-KLGGATAEIMSDLLAFEADRRAVNITINSIGTELTRDD-RRKLYS-LYPYGHEELAVCEDIDQVRGVMEKYPPYQSIFSKLSYGESQMLDKAFYEEEVKRLCLAFEQQFHYGVFFAYMRLREQEIRNLMWISEC-------------*FLVTTLVFLVIGIIASLCTRICCNRGPSTNLLHLTLVITATVSCWMMWAIVYLAQMKPLIVPILSE*ETAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRAGQ*E-TAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRAGQ-SR*E-TAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRAGQSRA*-ETAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMG-VMR--P-ELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRA-GQSR*ETAPFFGFLGAAAALVFSCMGAAYGTAKSGVGV-ASMG-VM--RPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRA-GQSR*---E-TAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILS-SR--AGQ-*--E-T-APFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRA-GQSR-*---ET--APFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRAGQSR*XXXXXX-XX-----------------------------------------------------------------------XX-XXX-XX-XXX-XXX-XX--X-----------------------------------------------------*TAPFFGFLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPELVMKSIVPVVMAGVLGIYGLIIAVIISTGINPKAKSYYLFDGYAHLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKLFVGMILILIFAEALALYGLIVGIILSSRAGQ*-------------------------------------------------------------*
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YGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMS-GTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD*-------NTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFY--*YGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMSG-TKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVA-N---GANWS--KL-ADSTGDVKHAVSSSKFFEPSRGEK-EVHGE--FEKLLSTMQERFAESTD*---------N-TVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFY--*YGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPELYTEMS-GTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVA-N----G--ANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAEST-D--*----------NTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFY--*LTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYG*SQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPS-*LTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVIS-NDYLNK-DLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYG*SQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPS*LTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRA-PLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYG*SQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPS*VFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRVMQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDFRLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPRTENTIAYINSELD-ELDREEFYRLKKVQEKKQNETA--K--L---*AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLF*MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDTLIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRKFKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVFINWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDKKGKINKQDTSLHQYASLVDTEYEPFVMYIINL*MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK*---VQLYIPLEV-IREVTFLLG--K--M----------------L--RRFDEVERMVGFLNEVVEKH---LSLENVNDMVKEITDCESRARQLDESLDSLRSKLNDLLEQRQVIFECS-KFIEV-------YMITGSIRRTKVDILNRILWRLLRGNLIFQNF-P--IE----V---E-KDCFIIFTHGETLLKKVKRVIDSLNG-KIVSLNT--RSSELVDTLNRQIDDLQRILDTTEQTLHTELLVIHDQLPVWSAMTKREKYVYTTLNKFQQESQ-GLIAEGWVPSTELIH-LQDSLKDYIE-T-LGSEYS-T-VFN-V-------------------------------AGLATVVTFPFMFAIMFGDMGHGFILFLMALFLVLNERKFGAMHRDEIFDMAFTGRYVLLLMGAFSVYTGLLYNDIFSKSMTIFK-SGWQWPST-FRKGESIEAKKT-GVYPFGLDFAWHGTDNGLLFSNSYKMKLSILMGYAHMTYSFMFSYINYRAKNSKVDIIGNFIPGLVFMQSIFGYLSWAIVYKWSKDWIKDDKPAPGLLNMLINMFLAPGTIDDQLYSGQAKLQVVLLLAALVCVPWLLLYKPLTLRRLNKFNFGDVMIHQVIHTIEFCLNCISHTASYLRLWALSLAHAQLSSVLWDMTISNAFSSKNSGSPLAVMKVVFLFAMWFVLTVCILVFMEGTSAMLHALRLHWVEAMSK--------------*ILSSIWTEGLLMCLIVSALLLFILIVALSWISNLDITYGALEKS*FSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ*GVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEIIRNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSDLLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY*FYTVVGVFIVVSAMSVLFWIM-AP-KNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVAPRRSDL*LCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQ*ELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV*ELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV*TELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALY---TGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV*ELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQ-ALY--TGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV*ELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQ---KQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC*ELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQ---KQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC*NIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVVAVLIAGNLSPT-EDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGS---*LCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV*--------------------------------------------------------------------------------------------------------------------------------------------------------*CCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAALVYLVFFVFCGFQ*

#Total CPU time is 674.55 seconds

Alignment between 6o7v (red) and 7uwb (blue)

If this cropped png is not good enough, open the pymol session of the two protein:

pixi run pymol results/comparison/7uwb-6o7w.usalign.sup.pse 

Determining the quality of an predicted complex

# Calculate the amount of steric clashes between two structures.
cp resources/examples/P60709_actin.pdb data
pixi run make results/mol/3b5u.clashes.csv results/mol/P60709_actin.clashes.csv

This gives the following results:

structure	clashes	clashes_percentage	frameid
results/input/3b5u.pdb	5	0.012176708392187425	0
results/input/P60709_actin.pdb	2799	5.318057455540356	0

This shows that the P60709_actin structure is not close to the crystal structure. An Ramachandran analysis, shows that the number of unique confirmations is lower in the predicted structure than in the crystal structure.

Ramachandran plot of 3b5u (left) and the predicted structure (right)