●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

DockRMSD is a program for the calculation of RMSD (root-mean-square deviation) between two poses of the same ligand molecule docked on the same protein structure without the assumption of known atomic ordering between the two files. This is achieved by recursively determining all possible atomic mappings between the two poses given their respective atomic bonding networks, and returning the mapping whose RMSD is the lowest. This is particularly relevant for comparing ligands with symmetric structure (e.g., benzene ring) as a simiple comparison based on default atomic ordering does not result in the minimum RMSD. DockRMSD does not perform any structural superposition; to calculate RMSD between two superimposed ligand conformations, see LS-align.

Note: This algorithm assumes that the two structure files represent two poses of the same ligand molecule, and that the two poses are oriented relative to aligned receptors.

Input Structure 1 in MOL2 format:
Please copy and paste your structure file here. Sample input

Or upload the stucture file:


Input Structure 2 in MOL2 format:
Please copy and paste your structure file here. Sample input

Or upload the stucture file:


Options:
Use hydrogens when calculating RMSD
Assume atomic correspondence between files

Input Email: (optional, where results will be sent to)

• Click DockRMSD.c to download the newest version of the source code of DockRMSD coded in C. You can compile the program on your Linux computer using:
  gcc DockRMSD.c -o DockRMSD -lm -O3
• Click DockRMSD.h to download a header file version of DockRMSD, which implements DockRMSD's functionality in an importable function compatible with any C/C++ program. (Note: the -lm flag is required when compiling a program that includes this header file).
• Click DockRMSD to download the compiled binary for Linux systems. Nevetheless, it is strongly recommended that users download the DockRMSD source code and compile it on your machine, which will optimize the speed of the program.
• Click data.tar.gz to download all manuscript related data.

• E.W. Bell, Y. Zhang. DockRMSD: an Open-Source Tool for Atom Mapping and RMSD calculation of Symmetric Molecules through Graph Isomorphism. Journal of Cheminformatics, 11:40 (2019). (PDF).