Abstract
We have developed an evolutionary approach for the flexible docking that is now an important component of a rational drug design. This automatic docking tool, referred to as the GEMDOCK (Generic Evolutionary Method for DOCKing molecules), combines both global and local search strategies search mechanisms. GEMDOCK used a simple scoring function to recognize compounds by minimizing the energy of molecular interactions. The interactive types of atoms between ligands and proteins of our linear scoring function consist only hydrogen-bonding and steric terms. GEMDOCK has been tested on a diverse dataset of 100 protein-ligand complexes from Protein Data Bank. In total 76% of these complexes, it obtained docked ligand conformations with root mean square derivations (RMSD) to the crystal ligand structures less than 2.0 A when the ligand was docked back into the binding site. Experiments shows that the scoring function is simple and efficiently discriminates between native and non-native docked conformations. This study suggests that GEMDOCK is a useful tool for molecular recognition and is a potential docking tool for protein structure variations.
Original language | English |
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Pages (from-to) | 2372-2383 |
Number of pages | 12 |
Journal | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
Volume | 2724 |
DOIs | |
State | Published - 18 Jun 2003 |
Keywords
- Molecular Docking
- Evolutionary Approach
- Rotatable Bond
- Family Father
- Gaussian Mutation