Chemical Structure Optimization

The molecules physiochemical properties are depends upon specific conformation. Thus suitable multi-conformer stuctures (2D/3D) of compounds to facilitate to selecting desired compounds. There are several tools are available to generate 2D/3D structure/conformers.

List of stoftware and web servers used for structure optimization of molecules:

Softwares Description
OpenbabelOpenbabel is a free software, used in the inter-conversion of chemical structure/conformers (2D/3D) and different chemical file formats, substructure search, force field calculation, extraction of stereochemical information and fingerprint calculation.
SMI23D SMI23D (3D Cordinate Generation) program converts one or more SMILIES strings into 3D.
FROGFROG (FRee Online druG) is a molecule conformation generation tool for small molecules starting from their 1D or 2D descriptions.
TINKER It is molecular modeling software having several features such as molecular dynamics, minimization and conformational sampling. It generates structure conformers by unconstrained molecular dynamics and each conformer is simulated and energy minimized.
MOPACMolecular Orbital PACkage (MOPAC) is an open source semi-empirical quantum chemistry program that is used to study molecular structures and reactions.
BalloonIt generates 3D atomic coordinates using molecular connectivity via distance geometry.
CyndiIt is based on the multi-objective evolution algorithm which is capable of generating geometrically diverse conformers at the large scale.
DG-AMMOS It used to generation of the 3D conformation of small molecules using distance geometry and their energy minimization.

List of commercial stoftware and web servers:

Softwares Description
AMBERAssisted Model Building with Energy Refinement (AMBER) is the molecular dynamics software package that measures force fields. It also used in geometry optimization of chemical structures.
GROMOSIT is a molecular dynamics simulation package used for simulation and geometry optimization.
VLifeMDSIt is advanced chemoinformatics tool offering Molecular docking, QSAR, 2D QSAR, 3D QSAR, Molecular modeling, Homology modeling and structure optimization.
YASARAYet Another Scientific Artificial Reality Application (YASARA) is a molecular visualisation, optimization, modelling, and dynamics program.
TREMOLO-XA Molecular Dynamics Software tool used in simulation, modeling and structure optimization.
MOEIt is chemoinformatics package used in Molecular Mechanics, Molecular Dynamics, optimization, Visualization, Automatic Pharmacophore Generation etc.
ICMIt is used in Molecular modeling and simulations, Homology and loop modeling, Protein-protein docking, Small molecule docking and screening and lead optimization.