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Research & Science · By JimLiu
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | 1.Esmfold2 Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. | JimLiu/ | 228 | 4 repos | ~2.5k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 2 | 2.Borzoi Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. | JimLiu/ | 228 | 4 repos | ~973 | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 3 | 3.Evo2 Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. | JimLiu/ | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 4 | 4.Scgpt Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. | JimLiu/ | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 5 | 5.Diffdock Predict small-molecule binding poses with DiffDock-L (Corso et al. | JimLiu/ | 228 | 4 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 6 | Generate a therapeutic indication dossier. An agent skill from JimLiu/science-skills. | JimLiu/ | 228 | 4 repos | ~1.4k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 7 | Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. | JimLiu/ | 228 | 4 repos | ~1.2k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 8 | 8.Boltz Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. | JimLiu/ | 228 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 9 | 9.Chai1 Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab). | JimLiu/ | 228 | 4 repos | ~1.2k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 10 | 10.Ligandmpnn Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. | JimLiu/ | 228 | 4 repos | ~1.5k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 11 | 11.Proteinmpnn Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. | JimLiu/ | 228 | 4 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 12 | 12.Scvi Tools Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. | JimLiu/ | 228 | 4 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 13 | 13.Solublempnn Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. | JimLiu/ | 228 | 4 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 14 | Find, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. | JimLiu/ | 228 | 4 repos | ~2.7k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
