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hgbrian / 1IGY_example.mol2
Created June 8, 2025 19:51
Example ligand for 1IGY
@<TRIPOS>MOLECULE
modal_out/afdesign/binder_1igy_cropped.fixed_B_CLKFYDDGSTRY_4.24.pdb_chain_B_model_1.pdb
102 105 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 N 9.4030 2.2140 39.8250 N.am 1 CYS1 -0.1954
2 CA 9.6790 3.4500 39.1080 C.3 1 CYS1 0.1843
3 C 11.1750 3.7370 39.0630 C.2 1 CYS1 0.2625
@hgbrian
hgbrian / mito_reads.fastq
Created June 8, 2025 11:10
example reads from human mitochondria
@example.1 1 length=200
GTTGATTACTATGGAAATAGCGGGTAGTAGCAGCTTGATTTTGAATTCAAGTTCTGATGATATATGAAGAAGGAGTGCCCTGAAGTAAGTTATGTTGTAATGAGNATTTTGGCNCAGTNTGGACNTGCCNNANNNNNNNNNNNNNGNNNNTNNNNNNNNNNNNNNNNNNNNNNNAGNNAANNNNNNNNNANANNNNNNNN
+example.1 1 length=200
CCCCCGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGCEG>GGGGGCGGGGECGGEGGGEEGGGE1@1DGFGDFGG0;FGGGG@F:BF0=E@@ECGGGCCCC#??EEGEAG#=@;=#00=D0#=<:E#######################################################################
@example.2 2 length=200
AAATAACCTTTAAGCTGACTTATTAATTGGATAGGTGAATTATTTTTATCTATTAAATTGTTATGGTTTATATTTTTATCGTTATAAGCATATAAACTATAAATTTTGAATCACAGTATATTTTATTTACAATTTTATCTTTTTGTAAGATAAGTGCTGGTATTTTAAGATCTTTTAATTTATTAAAGTATGTCTCTGAA
+example.2 2 length=200
B:AB@FGGGGGGDGGEGGGGGGFC@GGGGG:FDF>=1EGGGCGGGGGGG>FFGFGC@@F1FGDGEEG>G1C1FGFGG@GC0=F0=:0:00=:B0:00=;CBB@BBFFCFFFDG111;=F;==FFEFG1=<11==FGGF>1==1:9:11=1BF11<1:11111=1:D1<:CG1CGGD1<FE1:;1@F>0CDCDG0000=E0
@example.3 3 length=200
TCTTCAGTTTCCCCCAGCCTTTCTGCAATTCGCCGGAGAGAGCGAGTCATCATCCCCATCCAACTGATTAAATCTACGTGTAGCTCACCGGGGTGTGGGG
@hgbrian
hgbrian / mito.fasta
Created June 8, 2025 11:08
Homo sapiens mitochondrion, complete genome
>NC_012920.1 Homo sapiens mitochondrion, complete genome
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC
ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA
AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA
CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC
AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC
@hgbrian
hgbrian / regress_adaptyv_round_2.py
Created December 30, 2024 22:51
Regress Kd against other features for data from Adaptyv round 2
import polars as pl
import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.ensemble import RandomForestRegressor
from sklearn.svm import SVR
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import KFold
from sklearn.metrics import r2_score, mean_squared_error
from sklearn.inspection import permutation_importance
import xgboost as xgb
@hgbrian
hgbrian / boltz_bugs.md
Created November 30, 2024 18:23
Run Boltz through Gemini
  • src/boltz/data/parse/schema.py line 507: chain_type = const.chain_type_ids[entity_type.upper()]. The variable entity_type could be "ligand" in this branch, resulting in a KeyError. This should use the chain.type from the parsed_chain object.
--- a/src/boltz/data/parse/schema.py
+++ b/src/boltz/data/parse/schema.py
@@ -504,7 +504,7 @@
             parsed_chain = ParsedChain(
                 entity=entity_id,
                 residues=residues,
-                type=const.chain_type_ids["NONPOLYMER"],
@hgbrian
hgbrian / adaptyv_round_2_animation.py
Last active November 10, 2024 20:28
Script to make a video animation of adaptyv round 2 binders bound to EGFR
"""
Uses https://github.com/hgbrian/biomodals
Makes a video like https://www.youtube.com/watch?v=DJkY-Tkg8RE
Top 100 PDBs already folded here: https://drive.google.com/drive/folders/10JoYaVgFyJ_y3iPB9-JyryjpJFpbObKo?usp=sharing
Adaptyv round 2 fasta from https://raw.githubusercontent.com/agitter/adaptyvbio-egfr/refs/heads/main/round2/screening/adaptyv-egfr-design-competition-round2-400-seqs-2024-11-07.fasta
"""
from pathlib import Path
from subprocess import run
import prody as pd
@hgbrian
hgbrian / adaptyv_r2_EGFR.sh
Last active October 30, 2024 09:33
Adaptyv round 2 -- run BindCraft and RSO on EGFR domain 3
# with modal installed https://modal.com/docs/guide
git clone https://github.com/hgbrian/biomodals
cd biomodals
wget https://gist.githubusercontent.com/hgbrian/affd44dc63c6fb01a5a9620c24c74b26/raw/fac48e464dc3fe9d7224fe84ce1bd475667cba36/6aru_final_chain_A_domain_3.pdb
TIMEOUT=120 GPU=A100 modal run modal_bindcraft.py --input-pdb 6aru_final_chain_A_domain_3.pdb --number-of-final-designs 1
TIMEOUT=120 GPU=A100 modal run modal_rso.py --input-pdb 6aru_final_chain_A_domain_3.pdb --num-designs 5
@hgbrian
hgbrian / 6aru_final_chain_A_domain_3.pdb
Last active October 29, 2024 23:46
EGFR pdb 6aru, chain A, domain 3
ATOM 2374 N ARG A 310 30.035 29.295 35.478 1.00 29.00 N
ATOM 2375 CA ARG A 310 29.976 28.715 36.783 1.00 29.00 C
ATOM 2376 CB ARG A 310 28.581 28.145 37.025 1.00 29.00 C
ATOM 2377 CG ARG A 310 28.502 27.142 38.156 1.00 29.00 C
ATOM 2378 CD ARG A 310 27.112 27.031 38.759 1.00 29.00 C
ATOM 2379 NE ARG A 310 27.259 26.629 40.150 1.00 29.00 N
ATOM 2380 CZ ARG A 310 27.648 25.419 40.555 1.00 29.00 C
ATOM 2381 NH1 ARG A 310 27.907 24.441 39.694 1.00 29.00 N
ATOM 2382 NH2 ARG A 310 27.765 25.168 41.845 1.00 29.00 N
ATOM 2383 C ARG A 310 31.067 27.642 36.819 1.00 29.00 C
@hgbrian
hgbrian / Components-smiles-stereo-oe.smi
Created September 18, 2024 02:53
Components-smiles-stereo-oe.smi
This file has been truncated, but you can view the full file.
COC(=O)O 000 methyl hydrogen carbonate
COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4)(F)F 001 1-[2,2-difluoro-2-(3,4,5-trimethoxy-phenyl)-acetyl]-piperidine-2-carboxylic acid 4-phenyl-1-(3-pyridin-3-yl-propyl)-butyl ester
CC[C@H](C)[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)O)NC(=O)[C@H](Cc1ccccc1)CC(=O)NO 002 n-[(2r)-2-benzyl-4-(hydroxyamino)-4-oxobutanoyl]-l-isoleucyl-l-leucine
CC(C)CN1c2c(c(n(n2)Cc3cccc4c3cccc4)c5ccncc5)C(=O)N(C1=O)C 003 5-methyl-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-3-pyridin-4-yl-2h-pyrazolo[3,4-d]pyrimidine-4,6(5h,7h)-dione
c1ccc(cc1)[C@@H](C(=O)O)N 004 (2s)-amino(phenyl)ethanoic acid
c1ccc(cc1)C[C@@H]([C@@H](C(=O)O)O)N 005 (2s,3s)-3-amino-2-hydroxy-4-phenylbutanoic acid
Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C 006 (4r)-3-[(2s,3s)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-n-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
@hgbrian
hgbrian / pdbbind_pp.tsv
Created September 7, 2024 00:02
PDB Bind protein-protein binding data parsed into tsv
pdb_id resolution year kind value unit mer desc num_chains
1fc2 2.8 1981 Kd 7.647817481888637 nM 224 Human Fc fragment, Kd=22.5+/-4.6nM, SpAb-1 and Fc gamma-1, pKd=7.65 3
3sgb 1.8 1983 Kd 10.747146969020108 pM 56 TURKEY OVOMUCOID INHIBITOR (OMTKY3), 1.79 x 10-11M 2
2tgp 1.9 1983 Kd 5.619788758288394 uM 58 TRYPSIN INHIBITOR, 2.4 x 10-6M 2
2ptc 1.9 1983 Kd 13.221848749616356 fM 58 Kd=6x10-14M is for trypsin and the pancreatic trypsin inhibitor 2
2sni 2.1 1988 Kd 11.698970004336019 pM 83 CHYMOTRYPSIN INHIBITOR 2, Kd=2 x 10-12M 2
1atn 2.8 1992 Kd 9.346787486224656 nM 260 bovine pancreatic deoxyribonuclease I, Dnase I; Kd=0.45nM 3
1gla 2.6 1993 Kd 6.7447274948966935 uM 168 Glucose specific phosphocarrier, 1.8 x 10-7M 2
1acb 2.0 1993 Kd 9.698970004336019 nM 70 leech (Hirudo medicinalis) protein proteinase inhibitor eglin c, 2 x 10-10M 2
2pcc 2.3 1993 Kd 5.795880017344075 uM 108 yeast iso-1-cytochrome c, Kd=1.6uM, not found in reference 4