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4 results for “peptide binder”
Umbrella simulation data of designed cyclic peptide as MDM2 binders
<p>Umbrella simulation data of designed cyclic peptide as MDM2 binders.</p> <p>Pulling simulation: start from bound MDM2/ligand to pull the ligand out</p> <p>Pushing simulation: start from unbound ligand to push it bind to MDM2</p> <p>Details of umbrella simulation parameters can be found in simulation set-up folders.</p>
Design of linear and cyclic peptide binders
<p>The data is compressed with zstd: https://github.com/facebook/zstd and tar. To uncompress do: </p> <p>tar --use-compress-program full/path/to/zstd -xvf file.tar.zst</p> <p>PDB files of predicted protein-peptide complexes from the design process:</p> <p>1.1G 1ssc_untargeted_cyclic_afm.tar.zst <br>1.1G 1ssc_untargeted_cyclic.tar.zst<br>1.1G 1ssc_untargeted_linear_afm.tar.zst<br>1.1G 1ssc_untargeted_linear.tar.zst</p> <p>Selected PDB files of predicted protein-peptide complexes from the design process:</p> <p>(440 KB each). 1ssc_adversarial_linear_sel, 1ssc_tp_cyclic_sel, 1ssc_tp_linear_sel</p> <p>Metrics:</p> <p>1ssc_cyclic_merged_with_solubility.csv - all cyclic design metriccs</p> <p>1ssc_linear_merged_with_solubility.csv - all linear design metriccs</p> <p>1ssc_linear_adversarial_sel.csv - adversarial selection for linear design</p> <p>1ssc_linear_tp_sel.csv - top selection for linear design</p> <p>spr_results.csv - SPR affinities (Kd)</p> <p>1ssc_cyclic_tp_sel.csv - top selection for cyclic design</p> <p>linear_top_adversarial_pae.csv - PAE scores for linear top and adversarial designs</p>
Dataset for Peptide binder design with inverse folding and protein structure prediction
<p>Dataset for a paper on peptide design</p> <p> </p> <p><br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)</p> <p> </p> <p> </p>
Datasets for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder
<p>PepPC-F and PepPC Datasets for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder</p>
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