A new Lamarckian genetic algorithm for flexible ligand‐receptor docking

Abstract

We present a Lamarckian genetic algorithm (LGA) variant for flexible ligand-receptor docking which allows to handle a large number of degrees of freedom. Our hybrid method combines a multi-deme LGA with a recently published gradient-based method for local optimization of molecular complexes. We compared the performance of our new hybrid method to two non gradient-based search heuristics on the Astex diverse set for flexible ligand-receptor docking. Our results show that the novel approach is clearly superior to other LGAs employing a stochastic optimization method. The new algorithm features a shorter run time and gives substantially better results, especially with increasing complexity of the ligands. Thus, it may be used to dock ligands with many rotatable bonds with high efficiency.

Synthesis, structure, biochemical, and docking studies of a new dinitrosyl iron complex [Fe2(μ-SC4H3SCH2)2(NO)4]

“…The comparison of calculated and experimental bond lengths and angles was done for validity of QM approach, showing good fitness of theory to experiment (Table S2). Docking studies were performed using Autodock package [23] with LGA method [24,25]. As there is still no consensus about the oxidation states of iron and nitrosyl ligands in DNICs, docking parameters for NO and non H-bonding iron were evaluated in a simplified way using default Autodock atomic parameter file, considering the overall zero charge of DNICs.…”

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“…Kollman united atom charges were assigned to protein and PDBQT file was created. The 3-D affinity grid fields with grid map of 60 × 80 × 60 points were created using the auxiliary program AutoGrid 15,16 For evaluating binding energy in the docking step, Columbic electrostatic potential, vander waals interaction represented as a LennardJones12-6 dispersion/repulsion 12-10 term and hydrogen bonding represented as a directional 12-10 term were taken into account 17 . The resultant structure files were analyzed using PyMOL visualization programs.…”

Monocyclicβ-lactam and unexpected oxazinone formation: synthesis, crystal structure, docking studies and antibacterial evaluation

“…Lamarckian Genetic Algorithm was used to carry out the docking analysis 39 . For binding energy in the docking step, the Van der Waals interaction representing as a Lennard-Jones 12-6 dispersion/repulsion, the hydrogen bonding as a directional 12-10 term, and the Coulombic electrostatic potential for charges were used.…”