タンパク質の立体構造予測プログラム AlphaFold2 (https://github.com/google-deepmind/alphafold)の ベンチマーク 結果を掲載します。AlphaFold2 は、DeepMind社が開発したタンパク質の立体構造予測プログラムであり、アミノ酸配列からタンパク質の立体構造を高い精度で予測することができます。また、GPU を利用することで高速に処理することが可能です。
テストした入力ファイル
- T1050 A7LXT1, Bacteroides Ovatus, 779 residues
- NP_001362351.1 multiple PDZ domain protein isoform 6 [Homo sapiens] 2000 aa
- KAG8491920.1 hypothetical protein CXB51_015235 [Gossypium anomalum] 2000 aa
T1050 A7LXT1, Bacteroides Ovatus, 779 residues
>T1050 A7LXT1, Bacteroides Ovatus, 779 residues|
MASQSYLFKHLEVSDGLSNNSVNTIYKDRDGFMWFGTTTGLNRYDGYTFKIYQHAENEPGSLPDNYITDIVEMPDGRFWINTARGYVLFDKERDYFITDVTGFMKNLESWGVPEQVFVDREGNTWLSVAGEGCYRYKEGGKRLFFSYTEHSLPEYGVTQMAECSDGILLIYNTGLLVCLDRATLAIKWQSDEIKKYIPGGKTIELSLFVDRDNCIWAYSLMGIWAYDCGTKSWRTDLTGIWSSRPDVIIHAVAQDIEGRIWVGKDYDGIDVLEKETGKVTSLVAHDDNGRSLPHNTIYDLYADRDGVMWVGTYKKGVSYYSESIFKFNMYEWGDITCIEQADEDRLWLGTNDHGILLWNRSTGKAEPFWRDAEGQLPNPVVSMLKSKDGKLWVGTFNGGLYCMNGSQVRSYKEGTGNALASNNVWALVEDDKGRIWIASLGGGLQCLEPLSGTFETYTSNNSALLENNVTSLCWVDDNTLFFGTASQGVGTMDMRTREIKKIQGQSDSMKLSNDAVNHVYKDSRGLVWIATREGLNVYDTRRHMFLDLFPVVEAKGNFIAAITEDQERNMWVSTSRKVIRVTVASDGKGSYLFDSRAYNSEDGLQNCDFNQRSIKTLHNGIIAIGGLYGVNIFAPDHIRYNKMLPNVMFTGLSLFDEAVKVGQSYGGRVLIEKELNDVENVEFDYKQNIFSVSFASDNYNLPEKTQYMYKLEGFNNDWLTLPVGVHNVTFTNLAPGKYVLRVKAINSDGYVGIKEATLGIVVNPPFKLAAALQHHHHHH
ジョブの実行方法
python3 docker/run_docker.py \
–fasta_paths=T1050.fasta \
–model_preset=monomer \
–max_template_date=2024-04-01 \
–data_dir=[データファイルのディレクトリ] \
–output_dir=[出力結果先] \
–benchmark
ベンチマーク結果
| ベンチマークNo. | 2 |
| 機器の特徴 | (4) Intel Xeon Gold 6448H 2.4GHz 32C/64T + (4) NVIDIA RTX A6000 |
| ベンチマーク実施日 | 2024年4月27日 |
| 実行環境詳細 | HPC-ProServer DPeR960 CPU : (4) Intel Xeon Gold 6448H 2.4GHz 32C/64T Mem : 4096GB (64) 64GB DDR5 4800MHz SSD : 960GB SATA SSD GPU : (4) NVIDIA RTX A6000 OS : RockyLinux 8.9 NVIDIA Driver : 550.54.15 , CUDA 12.4 Docker version 26.0.1, build d260a54 データは、25GbpsネットワークのNFS領域に配置 |
| AlphaFold Version | 2.3.2 |
| timeコマンド | 0.13user 0.01system 1:24:08elapsed 0%CPU (0avgtext+0avgdata 26880maxresident)k 808inputs+0outputs (3major+5042minor)pagefaults 0swaps |
| timings.json | { “features”: 3951.729302883148, “process_features_model_1_pred_0”: 6.498595237731934, “predict_and_compile_model_1_pred_0”: 232.60038781166077, “process_features_model_2_pred_0”: 4.694603443145752, “predict_and_compile_model_2_pred_0”: 204.78236889839172, “process_features_model_3_pred_0”: 4.037086009979248, “predict_and_compile_model_3_pred_0”: 203.1477324962616, “process_features_model_4_pred_0”: 4.555547714233398, “predict_and_compile_model_4_pred_0”: 199.04012203216553, “process_features_model_5_pred_0”: 4.7832207679748535, “predict_and_compile_model_5_pred_0”: 181.64868569374084, “relax_model_2_pred_0”: 19.424469232559204 } |
| 備考 | features : 3951.729302883148 sec , features以外 : 1065.21281933784 sec GPUメモリ：約9GB使用 |
| ベンチマークNo. | 1 |
| 機器の特徴 | (2) Intel Xeon Gold 6430 2.1GHz 32C/64T + (2) NVIDIA RTX 6000 Ada |
| ベンチマーク実施日 | 2024年4月27日 |
| 実行環境詳細 | HPC-ProServer DPrR7960 CPU : (2) Intel Xeon Gold 6430 2.1GHz 32C/64T Mem : 512GB (16) 32GB DDR5 4800MHz SSD : 1TB M.2 NVMe GPU : (2) NVIDIA RTX 6000 Ada OS : RockyLinux 8.9 NVIDIA Driver : 550.54.15 , CUDA 12.4 Docker version 26.0.1, build d260a54 データは、25GbpsネットワークのNFS領域に配置 |
| AlphaFold Version | 2.3.2 |
| timeコマンド | 0.15user 0.01system 1:30:43elapsed 0%CPU (0avgtext+0avgdata 27152maxresident)k 0inputs+0outputs (0major+5101minor)pagefaults 0swaps |
| timings.json | { “features”: 4743.83895778656, “process_features_model_1_pred_0”: 5.070164918899536, “predict_and_compile_model_1_pred_0”: 146.5927164554596, “process_features_model_2_pred_0”: 4.10901141166687, “predict_and_compile_model_2_pred_0”: 130.53641939163208, “process_features_model_3_pred_0”: 3.5964343547821045, “predict_and_compile_model_3_pred_0”: 120.6664125919342, “process_features_model_4_pred_0”: 3.591764450073242, “predict_and_compile_model_4_pred_0”: 116.03167223930359, “process_features_model_5_pred_0”: 3.603001594543457, “predict_and_compile_model_5_pred_0”: 111.4774022102356, “relax_model_2_pred_0”: 22.427526473999023 } |
| 備考 | features : 4743.838958 sec , features以外 : 667.7025261 sec GPUメモリ：約9GB使用 |
NP_001362351.1 multiple PDZ domain protein isoform 6 [Homo sapiens] 2000 aa
>NP_001362351.1 multiple PDZ domain protein isoform 6 [Homo sapiens]
MLEAIDKNRALHAAERLQTKLRERGDVANEDKLSLLKSVLQSPLFSQILSLQTSVQQLKDQVNIATSATS
NIEYAHVPHLSPAVIPTLQNESFLLSPNNGNLEALTGPGIPHINGKPACDEFDQLIKNMAQGRHVEVFEL
LKPPSGGLGFSVVGLRSENRGELGIFVQEIQEGSVAHRDGRLKETDQILAINGQALDQTITHQQAISILQ
KAKDTVQLVIARGSLPQLVSPIVSRSPSAASTISAHSNPVHWQHMETIELVNDGSGLGFGIIGGKATGVI
VKTILPGGVADQHGRLCSGDHILKIGDTDLAGMSSEQVAQVLRQCGNRVKLMIARGAIEERTAPTALGIT
LSSSPTSTPELRVDASTQKGEESETFDVELTKNVQGLGITIAGYIGDKKLEPSGIFVKSITKSSAVEHDG
RIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGMKQEAELMSREDVTKDADLSPVNASII
KENYEKDEDFLSSTRNTNILPTEEEGYPLLSAEIEEIEDAQKQEAALLTKWQRIMGINYEIVVAHVSKFS
ENSGLGISLEATVGHHFIRSVLPEGPVGHSGKLFSGDELLEVNGITLLGENHQDVVNILKELPIEVTMVC
CRRTVPPTTQSELDSLDLCDIELTEKPHVDLGEFIGSSETEDPVLAMTDAGQSTEEVQAPLAMWEAGIQH
IELEKGSKGLGFSILDYQDPIDPASTVIIIRSLVPGGIAEKDGRLLPGDRLMFVNDVNLENSSLEEAVEA
LKGAPSGTVRIGVAKPLPLSPEEGYVSAKEDSFLYPPHSCEEAGLADKPLFRADLALVGTNDADLVDEST
FESPYSPENDSIYSTQASILSLHGSSCGDGLNYGSSLPSSPPKDVIENSCDPVLDLHMSLEELYTQNLLQ
RQDENTPSVDISMGPASGFTINDYTPANAIEQQYECENTIVWTESHLPSEVISSAELPSVLPDSAGKGSE
YLLEQSSLACNAECVMLQNVSKESFERTINIAKGNSSLGMTVSANKDGLGMIVRSIIHGGAISRDGRIAI
GDCILSINEESTISVTNAQARAMLRRHSLIGPDIKITYVPAEHLEEFKISLGQQSGRVMALDIFSSYTGR
DIPELPEREEGEGEESELQNTAYSNWNQPRRVELWREPSKSLGISIVGGRGMGSRLSNGEVMRGIFIKHV
LEDSPAGKNGTLKPGDRIVEAPSQSESEPEKAPLCSVPPPPPSAFAEMGSDHTQSSASKISQDVDKEDEF
GYSWKNIRERYGTLTGELHMIELEKGHSGLGLSLAGNKDRSRMSVFIVGIDPNGAAGKDGRLQIADELLE
INGQILYGRSHQNASSIIKCAPSKVKIIFIRNKDAVNQMAVCPGNAVEPLPSNSENLQNKETEPTVTTSD
AAVDLSSFKNVQHLELPKDQGGLGIAISEEDTLSGVIIKSLTEHGVAATDGRLKVGDQILAVDDEIVVGY
PIEKFISLLKTAKMTVKLTIHAENPDSQAVPSAAGAASGEKKNSSQSLMVPQSGSPEPESIRNTSRSSTP
AIFASDPATCPIIPGCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVYEEGAACKDGRLWAGDQILEV
NGIDLRKATHDEAINVLRQTPQRVRLTLYRDEAPYKEEEVCDTLTIELQKKPGKGLGLSIVGKRNDTGVF
VSDIVKGGIADADGRLMQGDQILMVNGEDVRNATQEAVAALLKCSLGTVTLEVGRIKAGPFHSERRPSQS
SQVSEGSLSSFTFPLSGSSTSESLESSSKKNALASEIQGLRTVEMKKGPTDSLGISIAGGVGSPLGDVPI
FIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSVVTGHQQEP
ASSSLSFTGLTSSSIFQDDLGPPQCKSITLERGPDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGR
LKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLS
ジョブの実行方法
python3 docker/run_docker.py \
–fasta_paths=MPDZ.fasta \
–model_preset=monomer \
–max_template_date=2024-04-01 \
–data_dir=[データファイルのディレクトリ] \
–output_dir=[出力結果先] \
–benchmark=true
ベンチマーク結果
| ベンチマークNo. | 3 |
| 機器の特徴 | (2) Intel Xeon Gold 6426Y 2.5GHz 16C/32T + (2) NVIDIA RTX A6000 |
| ベンチマーク実施日 | 2024年6月16日 |
| 実行環境詳細 | HPC-ProServer DPrR7960 CPU : (4) Intel Xeon Gold 6426Y 2.5GHz 16C/32T Mem : 256GB (8) 32GB DDR5 4800MHz SSD(sys) : 1TB NVMe SSD SSD(data) : 15.36TB U.2 NVMe SSD <= データはこの領域に配置 GPU : (2) NVIDIA RTX A6000 OS : RockyLinux 8.10 NVIDIA Driver : 555.42.02 Docker version 26.1.3, build b72abbb |
| AlphaFold Version | 2.3.2 |
| timeコマンド | 0.14user 0.01system 4:46:14elapsed 0%CPU (0avgtext+0avgdata 26736maxresident)k 3784inputs+792outputs (28major+4631minor)pagefaults 0swaps |
| timings.json | { “features”: 4821.1200931072235, “process_features_model_1_pred_0”: 17.36833930015564, “predict_and_compile_model_1_pred_0”: 1369.2554149627686, “predict_benchmark_model_1_pred_0”: 1302.739129781723, “process_features_model_2_pred_0”: 16.627148389816284, “predict_and_compile_model_2_pred_0”: 1242.8643596172333, “predict_benchmark_model_2_pred_0”: 1194.1714398860931, “process_features_model_3_pred_0”: 14.082069396972656, “predict_and_compile_model_3_pred_0”: 1218.4357559680939, “predict_benchmark_model_3_pred_0”: 1180.7467677593231, “process_features_model_4_pred_0”: 14.319541692733765, “predict_and_compile_model_4_pred_0”: 1214.740605354309, “predict_benchmark_model_4_pred_0”: 1180.8296961784363, “process_features_model_5_pred_0”: 13.722816944122314, “predict_and_compile_model_5_pred_0”: 1109.9322047233582, “predict_benchmark_model_5_pred_0”: 1074.2233765125275, “relax_model_1_pred_0”: 151.10685849189758 } |
| 備考 | features : 4821.1200931072235 sec , features以外 : 12315.16552 sec GPUメモリ：約29GB使用 |
KAG8491920.1 hypothetical protein CXB51_015235 [Gossypium anomalum] 2000 aa
>KAG8491920.1 hypothetical protein CXB51_015235 [Gossypium anomalum]
MSNTCSYHHQKTCLYWYLTLVFCFFSPFSVKSNELQILLDLKSALNKSTTTAFNSWQTPNSICTFNGITC
NHEGFITELDLSTQNLTGILPFDSLCKLPSLQKLSFGYNSLHGPITGELNNCVKLQYLDLGNNFFTGFFP
NISSLIQLKFLHLNKSGFSGKFPWKSLENFTDLAVLSIGDNPFDRFQFPDQIFKLKKLNWLYMANCCIEG
KIPSAIGDLIELINLELENNYLSGDIPMEISKLHNLWQLELYYNNLTGKLPVGLRNLTKLEFFDASANKL
EGNISEMGYLNNLVSLHLYQNKFTGEIPPEFGQFRKLVNLSLYENMLTGPLPENLGSWANFDYIDVSENS
LTGPIPPYMCKQGTMRGLLLVQNRFTGEIPASYGNCKTLKRFRVNNNSLSGVVPAGIWGLPMVDIIDIAY
NRFEGPITSDIKNAKVMSILSVGFNRLSGELPQEISKAISLVKIEVNDNKFSGKIPHGIGELKRLNILKF
HNNMLSGSIPESLCSCVSLSDINMAVNSLSGKIPSCLGSLATLNSLNLSLNELSGKIPESLSSLKLNLFD
LSYNRLAGPIPESLSIEAYNGSLVGNPGLCSSTDRSFKRCQMGSGMSKDVHTIIVCFVIGVTVLLVSIGC
FVYLKRTEKDKNGDAHSLKEESWDVKSFHVLTFTEDEILDSIKQENLIGKGGSGNVYKVMLSNRVELAVK
HIWNTKSNSRRKTRSSAPMLTKHDGKAKELEAEVRTLSSIRHVNVVKLYCSITSEDSSLLVYEYLPNGSL
WDRLHTSKKMELDWDTRYEIAIGAAKGLEYLHHGCEKPVLHRDVKSSNILLDEYLKPKISDFGLAKIVQA
TSSMGNDSTHVIAGTHGYIAPEYGYTCKVDEKSDVYSFGVVLLELVTGKKPIEQEYGENKDIVSWVGSNL
KGKESVLSIVDPKIPHAFKEDAMKVLKIAILCTTTLPALRPTMRRVVQMLKEAEPYRLVGIVIVSFELRS
FKQESRRNRIGAESHATLGRGGLEHRDKRPHGDELGEARRGDVAFLAAKQGCDVMMSKKVTSRQGDLLKM
APKAVFLFLMLLSFMFYSSKAIRQNQWQFFSIMKASLSGNPLSDWEVNEGASYCNFTGVSCNNEGYVESM
NFSGWSLAGNFPADVCSYLPELRVLDISRNNFRGNFLNGVVNCSVLEVFNMSSVYLNATFPDLSKTTSLR
VLDLSYNRFRGDFSMSITNLTNLEVLYINENDGLNLWQLPTNISRLTKLRIMVLTTCKLYGRIPASIGNM
TSLVDLELSGNFLSGQIPKELGLLKNLQQLELYYNQHLSGTIPEELGNLIELIDLDMSVNHLSGSIPTSI
CRLPKLQVLQLYNNSLTGEIPGVIANSTTLTTLSLYGNFLSGQVPQNLGQLSPMVILDLSENQLSGSLPT
EVCRGGKLLYLLVLDNKLSGKLPDSYADCESLVRFRVSNNYLEGPIPEGLLGLPHVSIIDLADNNFTGHF
PGSIGNARNLSELFMQNNKVSGAIPRKISRAINMVKIDLSNNLLSGSIPTEIGNLKKLNLLVLQGNKLSS
SIPNSLSLLKSLNVLDLSSNCLTGNIPESLSELLPNFINLSNNNLSGPIPLSLIEGGLMESFSGNPGLCA
TVHIRNFPICSSHAYNHKKQNSMWAIIISVIVITIAALLILKRCFSNQRAAMEHDETLSSLFCSYDMKSF
HKTYFDLNDILEAMVDKNIVGHGGSGTVYRIELRSGDVVAVKKLWSRTRKDSTAEDQLIIKKCLNTEVET
LGNIRHKNIVKLYSYFSNFNCHLLVYDYMPNGNLWDALHKGWFHLDWPNRHQIALGVAQGLAYLHHDLLP
PIIHRDIKSTNILLDINYQPKVADFGIAKVLKDSTSTIIAGTYGYLAPEYAYSNKATTKCDVYSFGVVLM
ELITGKKPVDADFGEYKNIVYWVTTKLDTKEGVMEVIDKNLSGSFKDEMIQVLRIAMCCTCKNPSQRPTM
NEVVQLLIQTDPCLTDPYKFSTKTREASNVTENQFEEVES
ジョブの実行方法
python3 docker/run_docker.py \
–fasta_paths=CXB51.fasta \
–model_preset=monomer \
–max_template_date=2024-04-01 \
–data_dir=[データファイルのディレクトリ] \
–output_dir=[出力結果先] \
–benchmark=true
ベンチマーク結果
| ベンチマークNo. | 4 |
| 機器の特徴 | (2) Intel Xeon Gold 6426Y 2.5GHz 16C/32T + (2) NVIDIA RTX A6000 |
| ベンチマーク実施日 | 2024年6月16日 |
| 実行環境詳細 | HPC-ProServer DPrR7960 CPU : (4) Intel Xeon Gold 6426Y 2.5GHz 16C/32T Mem : 256GB (8) 32GB DDR5 4800MHz SSD(sys) : 1TB NVMe SSD SSD(data) : 15.36TB U.2 NVMe SSD <= データはこの領域に配置 GPU : (2) NVIDIA RTX A6000 OS : RockyLinux 8.10 NVIDIA Driver : 555.42.02 Docker version 26.1.3, build b72abbb |
| AlphaFold Version | 2.3.2 |
| timeコマンド | 0.12user 0.01system 7:29:19elapsed 0%CPU (0avgtext+0avgdata 26700maxresident)k 13808inputs+360outputs (83major+4879minor)pagefaults 0swaps |
| timings.json | { “features”: 14510.03740644455, “process_features_model_1_pred_0”: 16.09257435798645, “predict_and_compile_model_1_pred_0”: 1369.8961718082428, “predict_benchmark_model_1_pred_0”: 1302.927805185318, “process_features_model_2_pred_0”: 20.470452547073364, “predict_and_compile_model_2_pred_0”: 1240.4826309680939, “predict_benchmark_model_2_pred_0”: 1192.4554507732391, “process_features_model_3_pred_0”: 19.54660701751709, “predict_and_compile_model_3_pred_0”: 1219.1449038982391, “predict_benchmark_model_3_pred_0”: 1180.6673691272736, “process_features_model_4_pred_0”: 19.771172761917114, “predict_and_compile_model_4_pred_0”: 1214.8154442310333, “predict_benchmark_model_4_pred_0”: 1179.734739780426, “process_features_model_5_pred_0”: 21.067474603652954, “predict_and_compile_model_5_pred_0”: 1111.5943937301636, “predict_benchmark_model_5_pred_0”: 1075.6471076011658, “relax_model_1_pred_0”: 153.08944416046143 } |
| 備考 | features : 14510.03740644455 sec , features以外 : 12337.40374 sec GPUメモリ：約29GB使用 |
