Published 2025 | Version v2
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In silico evolution of globular protein folds from random sequences (extended data)

Creators

Description

  • Example_1,2 (examples from Fig. 1 A-D)
  • pfes_data1.zip (PFES with indels)
          FASTA (final fasta files)
          PDB (final pdb files) 
          GTclust (clustering with GTalign)
          RUNS (additional data from PFES simulation)
                 run{n}/progress.log (all details from simulation)
                 run{n}/bestlog.tsv (protein with the best score from each generation)
                 run{n}/lineage.tsv (lineage of the best protein from the last generation)
                 run{n}/traj.pdb (pdb trajectory that of the evolving protein. Works with VMD v1.9.3)
                 run{n}/seqstr.png (changes of the secondary structures in the lineage)
                 run{n}/summary.png (summary plot with the score and other information during the simulation)
  • MD.tar.gz (MD simulation trajectories for proteins from pfes_data1)
  • pfes_data2.zip (PFES with fixed length, population size 100)
          run{n}/progress.log
          run{n}/bestlog.tsv
          run{n}/lineage.tsv
          run{n}/Secondary_structures.png
          run{n}/Summary.png
  • pfes_data3.zip (PFES with fixed length, population size 1000)
          run{n}/progress.log
          run{n}/bestlog.tsv
          run{n}/lineage.tsv
          run{n}/Secondary_structures.png
          run{n}/Summary.png
  • pfes_data4.zip (PFES_with_interaction)
          HTH (PFES interacting with helix-turn-helix domain)
          HNT (PFES interacting with the HNH domain of CAS9)      
  • pfes-alpha.zip (code used in this study)
  • b-test.zip (test simulations with different selection strengths)

Files

b-test.zip

Files (18.1 GB)

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Additional details

Software

Repository URL
https://github.com/sahakyanhk/pfes

References