m3triq 0.2.9 → 0.2.10
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- package/README.md +19 -2
- package/dist/cli.js +1 -1
- package/package.json +1 -1
package/README.md
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@@ -84,8 +84,25 @@ m3t md results <job-id>
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## Structure Prediction
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```bash
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m3t predict esmfold MKFLILLFNILCL...
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m3t predict alphafold2 MKFLILLFNILCL... # Accurate (~
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m3t predict esmfold MKFLILLFNILCL... # Fast (~10s, max 1024aa)
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m3t predict alphafold2 MKFLILLFNILCL... # Accurate (~15-20min, max 2048aa)
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# ESMFold2-Fast — monomer or multi-chain complex (self-hosted A100, max 2048aa total).
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# Beats AlphaFold3 on antibody-antigen DockQ from single sequence; returns pLDDT/pTM/ipTM.
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m3t predict esmfold2 --sequence MKFLILLFNILCL... # monomer
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m3t predict esmfold2 --chain A:EVQL... --chain B:DIQM... # complex (antibody-antigen, PPI)
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m3t predict esmfold2-batch inputs.json # fold N complexes (results in input order)
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# Boltz-2 — biomolecular complex (protein + DNA/RNA + ligand) with binding affinity
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m3t predict boltz2 --protein MKFL... --ligand "CC(=O)O" --rna GGUC...
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```
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## Protein Embeddings
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```bash
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# ESMC-6B per-residue embeddings + pseudo-perplexity (lower = more "natural" sequence)
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m3t embed esmc --sequence MKFLILLFNILCL... # single sequence
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m3t embed esmc --sequence SEQ1 --sequence SEQ2 # batch (repeatable, max 32)
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```
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## Protein Design
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package/dist/cli.js
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@@ -24,7 +24,7 @@ const program = new Command();
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program
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.name('m3t')
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.description('M3TRIQ — protein-ligand analysis from the terminal')
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.version('0.2.
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.version('0.2.10')
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.option('--json', 'Output as JSON (machine-readable)')
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.hook('preAction', (thisCommand) => {
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const opts = thisCommand.optsWithGlobals();
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