A fast flexible docking method using an incremental construction algorithm.
By Matthias Rarey, Bernd Kramer, Thomas Lengauer, Gerhard Klebe. 1996
Subfields: Evaluation & Benchmarks, Computational Chemistry & Drug Discovery
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Evaluation & Benchmarks
- Gerhard Klebe
- Mehmet Gönen
- Shengyou Huang
- Giulio Rastelli
- Luca Pinzi
- Holger Gohlke
- Xiaoqin Zou
- Yoshihiro Yamanishi
In Computational Chemistry & Drug Discovery
- Shengyou Huang
- Xiaoqin Zou
- Gerhard Klebe
- Stefano Moro
- Veronica Salmaso
- Ming-Jing Hwang
- Zhong-Ru Xie
- Adriano Defini Andricopulo
Citations in the corpus
- Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Surflex and FlexX are broadly used molecular docking programs using empirical scoring functions [31,39].”
- AutoGrow: A Novel Algorithm for Protein Inhibitor Design (2009, background): “AutoDock employs a Lamarckian genetic algorithm that is computationally intensive and time consuming; one study found that Auto-Dock was slower than DOCK, FleX, GOLD, and ICM (58).”
- Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (2003, methodology): “Table 2 shows the absolute and relative amount of surface area per side-chain buried upon complex formation, as calculated by the recursive icosahedra method.(70) The values were averaged over all 150 snapshots taken for binding free energy calculations, and the surface area in the unbound state was”
- Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization (2012, methodology): “Finally, we demonstrate the performance of our proposed method in three different scenarios: (i) exploratory data analysis using low-dimensional projections, (ii) predicting interactions for the out-of-sample drug compounds and (iii) predicting unknown interactions of the given network.”
- Fast Docking on Graphics Processing Units via Ray-Casting (2013, background): “Though some docking approaches carry out sampling by greedy algorithms (such as incremental construction [38]), the most common approaches involve either individual Monte Carlo trajectories that sample Cartesian space or approaches that generate optimal solutions from a population of candidate solut”