Folder and Files Representation:
- bzip structures: The bzip(276-351)wtATF4 structure files including bzip homodimer, G308A mutated bzip structure.
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forcefields: This folder has forcefield related files , forcefield information mentioned below.
- a99SBdisp.ff is force field used in MD simulation of bZIP, TAD and fulllengthATF4 protein(Activating Transcription Factor 4).
1. Water dispersion interactions strongly influence simulated structural properties of disordered protein states S Piana, AG Donchev, P Robustelli, DE Shaw The journal of physical chemistry B 119 (16), 5113-5123
2. Developing a molecular dynamics force field for both folded and disordered protein states P Robustelli, S Piana, DE Shaw Proceedings of the National Academy of Sciences 115 (21), E4758-E4766
3. Development of a force field for the simulation of single-chain proteins and protein–protein complexes. Journal of chemical theory and computation, 16(4), pp.2494-2507.
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parameters: All atom simulations parameters files (md.mdp,ions.mdp,minim.mdp,npt.mdp,nvt.mdp)
- In 'ions.mdp' file coulombtype was adjusted to PME
- md300_500K.mdp file is parameter file for simulated annealing.
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wtATF4_dimerstructure: The wtATF(1-351) structures files including monomer, and homodimer.
- fulllength_atf4_structures: The wtATF4(1-351) structure files
- "FL_ATF4(1-351)basin_high.pdb" file is wtATF4(1-351) , replica#3 convereged structure from basin
- atf4(123-351): This directory has structure files related to truncated mutation of ATF4(123-351)
- d110a_d90a_atf4: This directory has structure files related to double point mutation @ 90th and 110th position of wtATF4(1-351) from Aspartic acid to alanine.