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DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening
TLDR
DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. Expand
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AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
TLDR
We developed the program AMMOS for refining both, the 3D structures of the small molecules present in chemical libraries and the predicted receptor-ligand complexes through allowing partial to full atom flexibility through molecular mechanics optimization. Expand
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Modelling of a Roulette Wheel Selection Operator in Genetic Algorithms Using Generalized Nets
The apparatus of Generalized Nets (GN) is applied here to a description of a selection operator, which is one of the basic genetic algorithm operators. The GN model presented here describes rouletteExpand
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A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments
TLDR
We describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (viathe web service MTiOpenScreen), and molecular mechanics optimization. Expand
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Molecular dynamics simulation of the human estrogen receptor alpha: contribution to the pharmacophore of the agonists
TLDR
We report on molecular dynamics simulations of ERα to get a deeper structural insight into the agonist–receptor interactions and the pharmacophore pattern of compounds with agonistic activity. Expand
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Genetic operators' significance assessment in multi-population genetic algorithms
TLDR
Genetic algorithms are widely applied bioinspired optimisation technique that search for a global optimal solution via three main genetic operators, namely selection, crossover, and mutation. Expand
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Modelling of Fermentation Processes Based on State Decomposition
This paper presents an overview of implementation of state decomposition approach to modelling of Saccharomyces cerevisiae and Escherichia coli cultivation processes. This approach, so-calledExpand
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Purposeful Model Parameters Genesis in Multi-population Genetic Algorithm
TLDR
Proposed procedure for purposeful model parameters genesis, originally developed for simple genetic algorithm has been validated for multi-population genetic algorithm when it is applied for the purposes of parameter identification of S. cerevisiae fed-batch cultivation. Expand
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Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions.
Most of the benchmark studies on docking-scoring methods reported in the last decade conclude that no single scoring function performs well across different protein targets. In this study aExpand
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Tuning Genetic Algorithm Parameters to Improve Convergence Time
Fermentation processes by nature are complex, time-varying, and highly nonlinear. As dynamic systems their modeling and further high-quality control are a serious challenge. The conventionalExpand
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