Calculation of RMSD values between two ligand poses using web servers/tools

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#Web servers for calculation of RMSD values between a ligand poses. 
Please note: One pose should be a reference pose and another should be a query pose.


PLDbench: The RMSD value between two molecules can be calculated using PLDbench. There are four modules in this webserver.
  • Single: This module's functionality is limited to calculating RMSD for the 57 complexes utilized in the benchmarking study. Users must submit the docked pose of a ligand that corresponds to one of the 57 PDB-IDs offered in the drop down option in this module. It accepts three file formats: '.pdb', '.mol2', and '.sdf'. Users can choose the type of RMSD they want to compute. Standard heavy-atom RMSD, Hungarian (symmetry-corrected) heavy-atom RMSD, and Minimum-distance heavy-atom RMSD can all be calculated using this module. As a result, the Hungarian (symmetry-corrected) heavy-atom RMSD value is returned by default. 
Link for the server:https://webs.iiitd.edu.in/raghava/pldbench/single.php
  • Benchmark: Users could use this program to run a benchmark analysis on a set of docked poses that have been archived in '.zip' or '.tar' format. Users can provide a '.zip' file containing many poses of a ligand obtained by docking in a specific format. In the archive file, the name of the ligand should be in the format "PDBID CHAIN.predictedligand.mol2" (for example, ABCD C.predictedligand.mol2).
Link for the server: https://webs.iiitd.edu.in/raghava/pldbench/benchmark.php
  • Compare: This module was written to calculate the RMSD value between a ligand's original position and the pose obtained after docking. Users can upload the original and docked pose of a ligand in one of three file formats: PDB, MOL2, or SDF in order to calculate RMSD. Users will receive the RMSD value between two molecules if they submit their data.
Link for the server: https://webs.iiitd.edu.in/raghava/pldbench/compare.php
  • Dataset: Datasets utilized in the benchmarking study can be found on the server. Users can get Receptor, Crystal ligands, Minimized ligands, and CCD (chemical components dictionary) ligands '.zip' files from the Datasets area. Furthermore, the procedures are provided that were utilized to accomplish docking for the convenience of users. A dataset of 702 peptide-ligand complexes is provided that were used to examine residue preferences at the peptide-ligand interface. The Protein Data Bank (PDB) was used to collect and compile these complexes .
Link: https://webs.iiitd.edu.in/raghava/pldbench/dataset.php


DockRMSD: It is a programme for calculating RMSD (root-mean-square deviation) comparing two poses of the same ligand molecule docked to the same protein structure, even though the tool does not assume the positions of the ligand and protein are atomic ordered. However, it does not perform any structural superimpositions. The allowed input file format is '.mol2'. 

Link for the server: https://zhanglab.ccmb.med.umich.edu/DockRMSD/

This programme can be downloaded also. The steps and details are mentioned in the same link given above.

LS-align: It calculates RMSD between two superimposed ligand conformations. It is a structural comparison technique for ligand molecules at the atom level. The final atom-to-atom alignment is obtained by optimising the target function using an enhanced-greedy based, iterative heuristic search technique. The allowed input file format is '.mol2'.

The LS-align programme has two modules: 

  • Rigid-LS-align for comparing rigid-body ligand structures,
  • Flexi-LS-align for comparing flexible structures.
The Flexi-LS-align module, in particular, rotates flexible bond-angles to find optimal alignments of many alternative conformers of ligand molecules, allowing for the consideration of binding-induced conformational changes in ligand structure comparison and alignment.

Link for the server: https://zhanglab.dcmb.med.umich.edu/LS-align/

This programme can be downloaded also. The steps and details are mentioned in the same link given above.

AutoDock Tools: AutoDock Tools may also be used to determine the RMSD between two poses. To do the same, select both the conformations in Autodock Tools (ADT), right-click on one of them in the control panel, and select RMSD/Superimpose from the drop-down menu. It will give you with RMSD values.





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