Integrative modeling of NPC Basket

IMP and other scripts for integrative modeling of the yeast and mouse Nuclearpore Complex (NPC) basket

List of files and directories in Yeast_NPC_Basket:

• Yeast_NPC_Basket/data contains all input data for modeling

• Yeast_NPC_Basket/data/gmms/* GMM representation of the yeast basket cryo-et density map

• Yeast_NPC_Basket/data/alignments/* Generic Mlps and TPR coiled-coil alignments

• Yeast_NPC_Basket/data/alns/* Alignment between yeast and mouse proteins for occam restraint

• Yeast_NPC_Basket/data/fasta/* All fasta sequences of the models

• Yeast_NPC_Basket/data/pdbs/* All input pdb files of the models

• Yeast_NPC_Basket/output Default output directory for scripts

• Yeast_NPC_Basket/results Directory containing all output models, sampson analysis figures, clusters from RMSD based clustering, randomly selected frames for pdb-dev sumission, centroid models from RMSD clustering, PDB-Dev cif files

• Yeast_NPC_Basket/src IMP modeling script for Yeast NPC basket

List of files and directories in Mouse_NPC_Basket:

• Mouse_NPC_Basket/data contains all input data for modeling

• Mouse_NPC_Basket/data/gmms/* GMM representation of the yeast basket cryo-et density map

• Mouse_NPC_Basket/data/alignments/* Generic Mlps and Mlp1 coiled-coil alignments

• Mouse_NPC_Basket/data/fasta/* All fasta sequences of the models

• Mouse_NPC_Basket/data/pdbs/* All input pdb files of the models

• Mouse_NPC_Basket/data/xlinks/* All XL-MS crosslinks used for the models

• Mouse_NPC_Basket/output Default output directory for scripts

• Mouse_NPC_Basket/results Directory containing all output models, sampson analysis figures, clusters from RMSD based clustering, randomly selected frames for pdb-dev sumission, centroid models from RMSD clustering, PDB-Dev cif files

• Mouse_NPC_Basket/src IMP modeling script

Information

Author(s): Neelesh Soni