id: 1EDI_A

3D View

3D demonstration and comparison

All-atom RMSD per residue

Per-residue all-atom RMSD

All-atom RMSD

All-atom RMSD values for structure pairs

ΔSASA per residue (not minimized)

Per-residue difference in solvent-accessible surface area between the intact and modified structures (prior to EM analysis)

ΔSASA per residue (minimized)

Per-residue difference in solvent-accessible surface area between intact and modified EM-derived structures

Total SASA

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 shown for 4 versions of structure marked as in list below:

R: reference. Intact structure without substitution
RR: reference relaxed. Intact structure after energy minimization (EM)
M: Modified. Structure with substitutuion before EM
MR: modified relaxed. Structure with substitution 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 algorithm implemented in PyMol: https://pymol.org/