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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Molden 2.0: quantum chemistry meets proteins.

Gijs Schaftenaar¹, Elias Vlieg², Gert Vriend³

¹CMBI, Radboudumc, Nijmegen, The Netherlands. Gijs.Schaftenaar@radboudumc.nl.

Journal of Computer-Aided Molecular Design

|July 29, 2017

Summary

Molden software has seen continuous development since 1995, enhancing quantum chemistry calculations and enabling ligand preparation for drug design and protein docking.

Keywords:

Electron density Electrostatic potential Molecular modelling Molecular visualisation Protein manipulation Quantum mechanics

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Area of Science:

Computational Chemistry
Drug Discovery
Structural Biology

Background:

The Molden software package has been available since 1995, with its initial publication in 2000.
Ongoing development has focused on expanding its capabilities in computational chemistry and molecular modeling.

Purpose of the Study:

To detail the continuous improvements and novel features implemented in the Molden software.
To highlight the software's utility in advanced computational chemistry tasks.
To showcase its application in drug design and protein-ligand interactions.

Main Methods:

Continuous software development and feature implementation.
Broadened support for various quantum chemistry calculation outputs.
Development of tools for ligand preparation and protein interaction analysis.

Main Results:

Enhanced and expanded support for quantum chemistry calculations.
Novel features for preparing ligands for drug design software.
Improved capabilities for working with protein structures for ligand docking.

Conclusions:

Molden software has evolved significantly with ongoing development.
The software provides robust tools for computational chemistry, drug design, and structural biology applications.
Recent updates enhance its utility in complex molecular modeling tasks, including protein-ligand docking.