Journal ArticleDOI
A new, improved hybrid scoring function for molecular docking and scoring based on AutoDock and AutoDock Vina
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TLDR
The new hybrid scoring function performed better than the original functions, both on training and test sets of protein–ligand complexes, as measured by the non‐parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root‐mean‐square error (RMSE) between the experimental binding affinities and the docking scores.Abstract:
Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.read more
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Journal ArticleDOI
Structure-Based Virtual Screening: From Classical to Artificial Intelligence.
Eduardo Habib Bechelane Maia,Eduardo Habib Bechelane Maia,Letícia Cristina Assis,Tiago Alves de Oliveira,Alisson Marques Silva,Alex Gutterres Taranto +5 more
TL;DR: An overview of the challenges involved in the use of CADD to performSBVS, the areas where CADD tools support SBVS, a comparison between the most commonly used tools, and the techniques currently used in an attempt to reduce the time and cost in the drug development process are presented.
Journal ArticleDOI
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
TL;DR: It is found that ligand minimization has an important impact, reducing the performance difference between AutoDock and Vina, and is the best of all methods in terms of docking power.
Journal ArticleDOI
Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review.
Zhifeng Liu,Yujie Liu,Guangming Zeng,Binbin Shao,Ming Chen,Zhigang Li,Jiang Yilin,Yang Liu,Yu Zhang,Hua Zhong +9 more
TL;DR: The fundamental knowledge of molecular docking, such as its theory, available softwares and main databases, are summarized and shows promising application in the research of biodegradation.
Journal ArticleDOI
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search.
Diogo Santos-Martins,Leonardo Solis-Vasquez,Andreas F. Tillack,Michel F. Sanner,Andreas Koch,Stefano Forli +5 more
TL;DR: In this paper, an OpenCL implementation of AutoDock4 is presented, which leverages the highly parallel architecture of GPU hardware to reduce docking runtime by up to 350-fold with respect to a single-threaded process.
Journal ArticleDOI
Binding studies and biological evaluation of β-carotene as a potential inhibitor of human calcium/calmodulin-dependent protein kinase IV
Huma Naz,Parvez Khan,Mohd Tarique,Safikur Rahman,Abha Meena,Shahzaib Ahamad,Suaib Luqman,Asimul Islam,Faizan Ahmad,Md. Imtaiyaz Hassan +9 more
TL;DR: A strong binding affinity of β-carotene is reported with human calcium/calmodulin-dependent protein kinase IV using molecular docking, fluorescence binding and isothermal titration calorimetry methods, which provides a newer insight into the use ofβ- carotene in cancer prevention and protection via inhibition of CAMKIV by regulating the signaling pathways.
References
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Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
Journal ArticleDOI
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.
Journal ArticleDOI
Numerical Recipes in C: The Art of Scientific Computing
Mary C. Seiler,Fritz A. Seiler +1 more
Journal ArticleDOI
Benchmarking sets for molecular docking.
TL;DR: A directory of useful decoys (DUD), with 2950 ligands for 40 different targets, leading to a database of 98,266 compounds, which allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens.
Journal ArticleDOI
The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures.
TL;DR: The outcomes of this project have been organized into a Web-accessible database named the PDBbind database and led to a collection of binding affinity data (K(d), K(i), and IC(50) for a total of 1359 complexes.
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