id: 1EDI_A

3D View

3D demonstartion and comparison

All-atom RMSD per residue

Root-mean square deviations of all the atoms of structure by residue

All-atom RMSD

RMSD values of all atoms in structure pairs. Whole structure atoms displacement concerned

ΔSASA per residue (not minimized)

Solvent accessible surface area difference between pre-EM versions (intact and moified) of structure per residue

ΔSASA per residue (minimized)

Solvent accessible surface area difference between post-EM versions (intact and moified) of structure per residue

Total SASA

Comparison of total SASA for whole structure

Total Rg values

Radius of Gyration comparison for structure variants

All results (zip)

Download all the structures (.pdb), plots (.png) and data (.xlsx) as a single archive

Enqueued

You task is enqueued to be processed

Status: PENDING

Intact refinement

Intact structure refinement using SCPacker

Status: PENDING

Apply modification

Amino Acid residue replacement using SCPacker

Status: PENDING

Intact EM

Energy minimization of intact structure performed by GROMACS

Status: PENDING

Modified EM

Modified structure energy minimization performed with GROMACS

Status: PENDING

Result analysis

Analysis of the results, structure comparison, plots preparation

Status: PENDING

Result publication

Preparing report, making results available to download

Status: PENDING

Report description

The report presented above includes plots showing changes of protein chain geometrical indicators as a result of modification. Results are whown for four versions of structure marked as in list below:

R: reference. Intact structure without modification
RR: reference relaxed. Intact structure after energy minimization (EM)
M: Modified. Structure with PTM before EM
MR: modified relaxed. Structure with PTM after EM

Algorithms used to predict the results are:

SCPacker: predicting side-chains position after modification

Petrovskiy, D.V.; Nikolsky, K.S.; Rudnev, V.R.; Kulikova, L.I.; Butkova, T.V.; Malsagova, K.A.; Kopylov, A.T.; Kaysheva, A.L. Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications. Int. J. Mol. Sci. 2023, 24, 13431. https://doi.org/10.3390/ijms241713431

GROMACS energy minimisation steepest decent algorithm. Details: https://manual.gromacs.org/.../energy-minimization.html. Cite: https://manual.gromacs.org/.../preface.html

Calculated values uses hydrogen placing algorythm implemented in PyMol: https://pymol.org/