Compare Alphafold and RoseTTAFold on Fox compute cluster. 
Same SLURM configuration was used for all analysis

#SBATCH --time=10:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=96
#SBATCH --mem=1000G
#SBATCH --partition=accel --gpus=4

## Analysis on a single whole node with 
- Processor Model name: AMD EPYC 7552 48-Core Processor
- GPU: NVIDIA A100-PCIE-40GB 

## Command used 
### RoseTTAFold
module purge
module load RoseTTAFold/1.0.0.2

run_pyrosetta_fox.sh query.fasta .
predict_complex.py -i t000_.msa0.a3m -o complex -Ls 218 310 

### Alphafold
module load Alphafold/2.0.0.1
#module load AlphaFold/2.0.0-fosscuda-2020b

ALPHAFOLD_DATA=/cluster/shared/databases/AlphaFold/full
run.sh -d $ALPHAFOLD_DATA  -o out -m model_1,model_2,model_3, model_4,model_5 -f query.fasta -t 2020-05-14


## Time comparisen

| Protein           |# of AA    | Alphafold    | RoseTTAFold  |
| -------------     |---------: |:-------------:| -----:|
| UniProt-O76024    |905	| 01:44:44 |  2:24:53|
| UniProt-P16736    |972	| 02:15:13 |  4:20:47|
| UniProt-P35575    |363	| 00:51:58 |  1:10:13|
| UniProt-Q9HVT1    |216	| 00:39:17 |  0:45:57|
| UniProt-Q9HVT1_No |196	| 00:38:44 |  0:46:53|
                    

## Sequences
>sp|O76024|WFS1_HUMAN Wolframin
MDSNTAPLGPSCPQPPPAPQPQARSRLNATASLEQERSERPRAPGPQAGPGPGVRDAAAP
AEPQAQHTRSRERADGTGPTKGDMEIPFEEVLERAKAGDPKAQTEVGKHYLQLAGDTDEE
LNSCTAVDWLVLAAKQGRREAVKLLRRCLADRRGITSENEREVRQLSSETDLERAVRKAA
LVMYWKLNPKKKKQVAVAELLENVGQVNEHDGGAQPGPVPKSLQKQRRMLERLVSSESKN
YIALDDFVEITKKYAKGVIPSSLFLQDDEDDDELAGKSPEDLPLRLKVVKYPLHAIMEIK
EYLIDMASRAGMHWLSTIIPTHHINALIFFFIVSNLTIDFFAFFIPLVIFYLSFISMVIC
TLKVFQDSKAWENFRTLTDLLLRFEPNLDVEQAEVNFGWNHLEPYAHFLLSVFFVIFSFP
IASKDCIPCSELAVITGFFTVTSYLSLSTHAEPYTRRALATEVTAGLLSLLPSMPLNWPY
LKVLGQTFITVPVGHLVVLNVSVPCLLYVYLLYLFFRMAQLRNFKGTYCYLVPYLVCFMW
CELSVVILLESTGLGLLRASIGYFLFLFALPILVAGLALVGVLQFARWFTSLELTKIAVT
VAVCSVPLLLRWWTKASFSVVGMVKSLTRSSMVKLILVWLTAIVLFCWFYVYRSEGMKVY
NSTLTWQQYGALCGPRAWKETNMARTQILCSHLEGHRVTWTGRFKYVRVTDIDNSAESAI
NMLPFFIGDWMRCLYGEAYPACSPGNTSTAEEELCRLKLLAKHPCHIKKFDRYKFEITVG
MPFSSGADGSRSREEDDVTKDIVLRASSEFKSVLLSLRQGSLIEFSTILEGRLGSKWPVF
ELKAISCLNCMAQLSPTRRHVKIEHDWRSTVHGAVKFAFDFFFFPFLSAA


>sp|P16736|HELI_HCMVA DNA replication helicase
MSMTASSSTPRPTPKYDDALILNLSSAAKIERIVDKVKSLSRERFAPEDFSFQWFRSISR
VERTTDNNPSAATTAAATTTVHSSASSSAAAAASSEAGGTRVPCVDRWPFFPFRALLVTG
TAGAGKTSSIQVLAANLDCVITGTTVIAAQNLSAILNRTRSAQVKTIYRVFGFVSKHVPL
ADSAVSHETLERYRVCEPHEETTIQRLQINDLLAYWPVIADIVDKCLNMWERKAASASAA
AAAAACEDLSELCESNIIVIDECGLMLRYMLQVVVFFYYFYNALGDTRLYRERRVPCIIC
VGSPTQTEALESRYDHYTQNKSVRKGVDVLSALIQNEVLINYCDIADNWVMFIHNKRCTD
LDFGDLLKYMEFGIPLKEEHVAYVDRFVRPPSSIRNPSYAAEMTRLFLSHVEVQAYFKRL
HEQIRLSERHRLFDLPVYCVVNNRAYQELCELADPLGDSPQPVELWFRQNLARIINYSQF
VDHNLSSEITKEALRPAADVVATNNSSVQAHGGGGSVIGSTGGNDETAFFQDDDTTTAPD
SRETLLTLRITYIKGSSVGVNSKVRACVIGYQGTVERFVDILQKDTFIERTPCEQAAYAY
SLVSGLLFSAMYYFYVSPYTTEEMLRELARVELPDVSSLCAAAAATAAAPAWSGGENPIN
NHVDADSSQGGQSVPVSQRMEHGQEETHDIPCLSNHHDDSDAITDAELMDHTSLYADPFF
LKYVKPPSLALLSFEETVHMYTTFRDIFLKRYQLMQRLTGGRFATLPLVTYNRRNVVFKA
NCQISSQTGSFVGMLSHVSPAQTYTLEGYTSDNVLSLPSDRHRIHPEVVQRGLSRLVLRD
ALGFLFVLDVNVSRFVESAQGKSLHVCTTVDYGLTSRTAMTIAKSQGLSLEKVAVDFGDH
PKNLKMSHIYVAMSRVTDPEHLMMNVNPLRLPYEKNTAITPYICRALKDKRTTLIF


>sp|P35575|G6PC1_HUMAN Glucose-6-phosphatase catalytic subunit 1
MEEGMNVLHDFGIQSTHYLQVNYQDSQDWFILVSVIADLRNAFYVLFPIWFHLQEAVGIK
LLWVAVIGDWLNLVFKWILFGQRPYWWVLDTDYYSNTSVPLIKQFPVTCETGPGSPSGHA
MGTAGVYYVMVTSTLSIFQGKIKPTYRFRCLNVILWLGFWAVQLNVCLSRIYLAAHFPHQ
VVAGVLSGIAVAETFSHIHSIYNASLKKYFLITFFLFSFAIGFYLLLKGLGVDLLWTLEK
AQRWCEQPEWVHIDTTPFASLLKNLGTLFGLGLALNSSMYRESCKGKLSKWLPFRLSSIV
ASLVLLHVFDSLKPPSQVELVFYVLSFCKSAVVPLASVSVIPYCLAQVLGQPHKKSL

>sp|Q9HVT1|Y4490_PSEAE
MRRLTAFGLALLLLASGVARGEPAVTLDPQQSQVFRAWFVRIAQEQLRQGPSPRWHQQDC
AGLVRFAANEALKVHDGKWLRANGLSNRYLPPELALSPEQRRLAQNWQQGGGQVGPYVNA
IKLVQFNSRLVGRDLNQARPGDLMFYDQGDDQHLMIWMGRSIAYHTGSSTPTDNGMRSVS
LQQLMTWKDTRWIPDESNPNFIGIYRLAFLSQ


>Q9HVT1_NoSignalPeptide
GEPAVTLDPQQSQVFRAWFVRIAQEQLRQGPSPRWHQQDC
AGLVRFAANEALKVHDGKWLRANGLSNRYLPPELALSPEQRRLAQNWQQGGGQVGPYVNA
IKLVQFNSRLVGRDLNQARPGDLMFYDQGDDQHLMIWMGRSIAYHTGSSTPTDNGMRSVS
LQQLMTWKDTRWIPDESNPNFIGIYRLAFLSQ