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adaptyvbio/protein-design-skills

24 skills · 842 combined installs

Skills from this source

#
Skill
Source
8W Activity
Installs
1
alphafold Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequence…
adaptyvbio/protein-design-skills
46
2
pdb Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, …
adaptyvbio/protein-design-skills
46
3
protein-design-workflow End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2)…
adaptyvbio/protein-design-skills
46
4
proteinmpnn Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffus…
adaptyvbio/protein-design-skills
46
5
cell-free-expression Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troublesho…
adaptyvbio/protein-design-skills
44
6
binder-design Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindC…
adaptyvbio/protein-design-skills
43
7
protein-qc Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quali…
adaptyvbio/protein-design-skills
43
8
campaign-manager Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete bin…
adaptyvbio/protein-design-skills
40
9
ipsae Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder d…
adaptyvbio/protein-design-skills
40
10
chai Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting pr…
adaptyvbio/protein-design-skills
39
11
uniprot Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences b…
adaptyvbio/protein-design-skills
39
12
binding-characterization Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (…
adaptyvbio/protein-design-skills
38
13
boltz Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predic…
adaptyvbio/protein-design-skills
38
14
foldseek Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases,…
adaptyvbio/protein-design-skills
38
15
boltzgen All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from th…
adaptyvbio/protein-design-skills
35
16
esm ESM protein language models for embeddings, sequence scoring, structure prediction, and binder design. Use this skill…
adaptyvbio/protein-design-skills
33
17
ligandmpnn Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small mole…
adaptyvbio/protein-design-skills
33
18
rfdiffusion Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure genera…
adaptyvbio/protein-design-skills
33
19
bindcraft End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built…
adaptyvbio/protein-design-skills
32
20
setup First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Com…
adaptyvbio/protein-design-skills
32
21
solublempnn Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expres…
adaptyvbio/protein-design-skills
31
22
germinal De novo antibody and nanobody (VHH) design with Germinal. Use this skill when: (1) Designing epitope-targeted nanobod…
adaptyvbio/protein-design-skills
9
23
mosaic Multi-objective, gradient-based protein binder design with Mosaic. Use this skill when: (1) Composing several structu…
adaptyvbio/protein-design-skills
9
24
protenix Structure prediction with Protenix, an open AlphaFold3 reproduction. Use this skill when: (1) Predicting complex stru…
adaptyvbio/protein-design-skills
9