MassivelyParallelFreeEnergyCalculationsofHABinders2024

This repository has most of the data and scripts that are necesarry to reproduce analysis and figures in Novack, D.; Zhang, S.; Voelz, V. A. Massively Parallel Free Energy Calculations for in Silico Affinity Maturation of Designed Miniproteins. bioRxiv May 18, 2024, p 2024.05.17.594758.. Additional data needed can be found at https://osf.io/sj6mr/. The jupyter notebooks in each folder will reproduce the publication figures stated below.

Contents:

data: Contains most of the data to reproduce figures from Novack, D.; Zhang, S.; Voelz, V. A. Massively Parallel Free Energy Calculations for in Silico Affinity Maturation of Designed Miniproteins. bioRxiv May 18, 2024, p 2024.05.17.594758.. Additional data for Figures YYYY can be found here -> https://osf.io/sj6mr/

Figures: These directories contain ipython notebooks to reproduce figure images from XXX, as well as having copies of figure images in them.

• Figure 3:
  • Alchemical_number - Fig. 3 /Supplementary Fig. 1
  • Charge_change - Fig. 3 /Supplementary Fig. 2
  • uncertainty_analysis -Supplementary Fig. 3
• Figure 4: Additional files can be found at https://osf.io/sj6mr/
  • ITS - Fig.4/Supplementary Fig. 3
• Figure 5:
  • Bayesian_Kds - Fig. 5
• Figure 6:
  • scatter_and_heatmaps - Fig. 6
• Figure 7:
  • scatter_and_heatmaps - Fig. 7
• Figure 8:
  • MCC_Conf - Fig. 8/Supplementary Fig. 3
• Figure 9:
  • Avg_Effects - Fig.9
• Figure 10:
  • Affinity_maturation - fig. 10
• Figure 11: Additional files can be found at https://osf.io/sj6mr/
  • multimutant - Fig.11/Supplentary Fig. 10
• SI:
  • Contact_Maps - Supplementary Fig. 3 - Supplementary Fig. 5
  • SI_simulated_tempering - Supplementary Fig. 8
  • laplacian_centrality - Supplementary Fig. 9-10 Additional files can be found at https://osf.io/sj6mr/