A new approach for flexible protein-ligand docking based on Particle Swarm Optimisation
Chemistry Central Journal ,
Mar 2008
Rene Meier , Frank Brandt , Teresa M Pisabarro , Carsten Baldauf
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A new approach for flexible protein-ligand docking based on Particle Swarm Optimisation
Chemistry Central Journal
Poster presentation A new approach for flexible protein-ligand docking based on Particle Swarm Optimisation
Rene Meier 0 2
Frank Brandt 0 1
Teresa M Pisabarro 0 1
Carsten Baldauf 0 1
Wolfgang Sippl 0 2
0 References 1. Wang R , Lai L, Wang S: J Comput-Aided Mol Des 2002, 16:11-26
1 Structural Bioinformatics , Biotec TU Dresden, Tatzberg 47-51, 01307 Dresden , Germany
2 Institute for Pharmaceutical Chemistry, Martin-Luther-University Halle-Wittenberg Wolfgang-Langenbeckstr. 4, 06120 Halle (Saale) , Germany
from 3rd German Conference on Chemoinformatics Goslar, Germany. 11-13 November 2007
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Particle Swarm Optimiser (PSO) uses a general-purpose,
iterative, heuristic search algorithm. It considers a
population of individuals to probe promising regions of the
search space in an effective manner. In this context, the
population of solutions is called a swarm, and the
individuals are called particles. Each particle moves within the
search space and retains in its memory the best position
and the overall best position that has been encountered.
The velocity of each particle is adjusted during each
iteration toward the personal best position as well as the
overall best position, thus mimicking swarm intelligence. In
our recent work we have implemented PSO in a
liganddocking program. The fitness landscape of the docking
program is modeled by a modified version of the scoring
function X-Score [1]. X-Score is an empirical scoring
function which shows a significant correlation between
calculated docking scores and experimentally derived ligand
geometries. Preliminary investigations show promising
results in terms of speed and accuracy. Special attention
during the development will be paid to a modular design
of the program in order to easily implement different
scoring functions as well as to perform parallel computing. (...truncated)
This is a preview of a remote PDF: https://link.springer.com/content/pdf/10.1186%2F1752-153X-2-S1-P6.pdf
Rene Meier, Frank Brandt, Teresa M Pisabarro, Carsten Baldauf.
A new approach for flexible protein-ligand docking based on Particle Swarm Optimisation ,
Chemistry Central Journal,
2008, pp. P6, Volume 2, Issue S1, DOI: 10.1186/1752-153X-2-S1-P6