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
Openbabel	Openbabel 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.
FROG	FROG (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.
MOPAC	Molecular Orbital PACkage (MOPAC) is an open source semi-empirical quantum chemistry program that is used to study molecular structures and reactions.
Balloon	It generates 3D atomic coordinates using molecular connectivity via distance geometry.
Cyndi	It 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
AMBER	Assisted 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.
GROMOS	IT is a molecular dynamics simulation package used for simulation and geometry optimization.
VLifeMDS	It is advanced chemoinformatics tool offering Molecular docking, QSAR, 2D QSAR, 3D QSAR, Molecular modeling, Homology modeling and structure optimization.
YASARA	Yet Another Scientific Artificial Reality Application (YASARA) is a molecular visualisation, optimization, modelling, and dynamics program.
TREMOLO-X	A Molecular Dynamics Software tool used in simulation, modeling and structure optimization.
MOE	It is chemoinformatics package used in Molecular Mechanics, Molecular Dynamics, optimization, Visualization, Automatic Pharmacophore Generation etc.
ICM	It is used in Molecular modeling and simulations, Homology and loop modeling, Protein-protein docking, Small molecule docking and screening and lead optimization.