examples/alphafold_monomer.sh
... ...
@@ -0,0 +1,24 @@
1
+#!/bin/bash
2
+
3
+ALPHAFOLD_X=2.3.2
4
+
5
+input=$1
6
+
7
+mkdir -p $(pwd)/$ALPHAFOLD_X
8
+
9
+/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \
10
+ --data_dir=/programs/local/alphafold-2.3.2 \
11
+ --output_dir=$(pwd) \
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+ --fasta_paths=${input} \
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+ --max_template_date=2020-05-14 \
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+ --db_preset=full_dbs \
15
+ --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 \
16
+ --uniref30_database_path=/programs/local/alphafold-2.3.2/uniref30/UniRef30_2021_03 \
17
+ --bfd_database_path=/programs/local/alphafold-2.3.2/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
18
+ --uniref90_database_path=/programs/local/alphafold-2.3.2/uniref90/uniref90.fasta \
19
+ --mgnify_database_path=/programs/local/alphafold-2.3.2/mgnify/mgy_clusters_2022_05.fa \
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+ --template_mmcif_dir=/programs/local/alphafold-2.3.2/pdb_mmcif/mmcif_files \
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+ --obsolete_pdbs_path=/programs/local/alphafold-2.3.2/pdb_mmcif/obsolete.dat \
22
+ --use_gpu_relax=True \
23
+ --model_preset=monomer
24
+
examples/alphafold_multimer.sh
... ...
@@ -0,0 +1,25 @@
1
+#!/bin/bash
2
+
3
+ALPHAFOLD_X=2.3.2
4
+
5
+input=$1
6
+
7
+mkdir -p $(pwd)/$ALPHAFOLD_X
8
+
9
+/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \
10
+ --data_dir=/programs/local/alphafold-2.3.2 \
11
+ --output_dir=$(pwd) \
12
+ --fasta_paths=${input} \
13
+ --max_template_date=2020-05-14 \
14
+ --db_preset=full_dbs \
15
+ --uniref30_database_path=/programs/local/alphafold-2.3.2/uniref30/UniRef30_2021_03 \
16
+ --bfd_database_path=/programs/local/alphafold-2.3.2/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
17
+ --uniref90_database_path=/programs/local/alphafold-2.3.2/uniref90/uniref90.fasta \
18
+ --mgnify_database_path=/programs/local/alphafold-2.3.2/mgnify/mgy_clusters_2022_05.fa \
19
+ --template_mmcif_dir=/programs/local/alphafold-2.3.2/pdb_mmcif/mmcif_files \
20
+ --uniprot_database_path=/programs/local/alphafold-2.3.2/uniprot/uniprot.fasta \
21
+ --pdb_seqres_database_path=/programs/local/alphafold-2.3.2/pdb_seqres/pdb_seqres.txt \
22
+ --obsolete_pdbs_path=/programs/local/alphafold-2.3.2/pdb_mmcif/obsolete.dat \
23
+ --use_gpu_relax=True \
24
+ --model_preset=multimer
25
+
examples/pasb_dimer.fasta
... ...
@@ -0,0 +1,5 @@
1
+>3H7W_1
2
+GEFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN
3
+>3H7W_2
4
+GEFKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE
5
+
examples/pasb_monomer.fasta
... ...
@@ -0,0 +1,2 @@
1
+>3H7W_1
2
+GEFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN