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Related Experiment Video

Updated: Jul 15, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Frog: a FRee Online druG 3D conformation generator.

T Bohme Leite¹, D Gomes, M A Miteva

¹Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR 726, Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris cedex 05, France.

Nucleic Acids Research

|May 9, 2007

Summary

Frog is a free online service that generates 3D molecular structures from 1D or 2D chemical data. This tool aids drug discovery by creating essential 3D models for virtual screening and computational studies.

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Area of Science:

Computational Chemistry
Drug Discovery
Cheminformatics

Background:

In silico screening methods are crucial for drug discovery, requiring 3D structures of ligands and proteins.
Generating multi-conformer 3D models is essential for efficient virtual screening and docking studies.
Many compound collections are available in 1D SMILES or 2D SDF formats, necessitating 1D/2D to 3D conversion tools.

Purpose of the Study:

To introduce Frog, an online service for generating 3D conformations of drug-like compounds from 1D or 2D descriptions.
To provide a free and accessible tool for creating 3D molecular models required for computational drug discovery.

Main Methods:

Frog utilizes atomic constitution and connectivity information to identify molecular isomers.
It employs an assembly process to generate single or multiple low-to-medium energy 3D conformations.

Related Experiment Videos

Last Updated: Jul 15, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

The method does not currently account for ring flexibility in its conformational generation.

Main Results:

Frog successfully generates 3D conformations for drug-like compounds from 1D/2D input formats.
Generated conformations are shown to be close to experimentally observed bioactive structures in crystallographic complexes.
The service provides an efficient way to obtain necessary 3D models for virtual screening.

Conclusions:

Frog is a valuable free online resource for generating 3D molecular conformations.
It addresses the need for 1D/2D to 3D structure generation in drug discovery workflows.
The tool facilitates virtual screening and other structure-based computational studies.