Related references
Note: Only part of the references are listed.Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions
Chao Shen et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Learning from the ligand: using ligand-based features to improve binding affinity prediction
Fergus Boyles et al.
BIOINFORMATICS (2020)
Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set?
Minyi Su et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets
Jincai Yang et al.
FRONTIERS IN PHARMACOLOGY (2020)
Generative Network Complex for the Automated Generation of Drug-like Molecules
Kaifu Gao et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
D. Vijay Anand et al.
SCIENTIFIC REPORTS (2020)
Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
Maciej Wojcikowski et al.
BIOINFORMATICS (2019)
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
Duc Duy Nguyen et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2019)
AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening
Duc Duy Nguyen et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Discrete Ricci curvatures for directed networks
Emil Saucan et al.
CHAOS SOLITONS & FRACTALS (2019)
Comparative Assessment of Scoring Functions: The CASF-2016 Update
Minyi Su et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks
Kelin Xia et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2019)
Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations
Robin Winter et al.
CHEMICAL SCIENCE (2019)
Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction
Zixuan Cang et al.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING (2018)
Breaking the polar-nonpolar division in solvation free energy prediction
Bao Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)
Development and evaluation of a deep learning model for protein-ligand binding affinity prediction
Marta M. Stepniewska-Dziubinska et al.
BIOINFORMATICS (2018)
Protein pocket detection via convex hull surface evolution and associated Reeb graph
Rundong Zhao et al.
BIOINFORMATICS (2018)
Improving classical scoring functions using random forest: The non-additivity of free energy terms' contributions in binding
Karim Afifi et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2018)
Machine learning in chemoinformatics and drug discovery
Yu-Chen Lo et al.
DRUG DISCOVERY TODAY (2018)
Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks
Kedi Wu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
Jose Jimenez et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility
Kedi Wu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)
Computer-calculated compounds
Nic Fleming
NATURE (2018)
Comparative analysis of two discretizations of Ricci curvature for complex networks
Areejit Samal et al.
SCIENTIFIC REPORTS (2018)
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
Zixuan Cang et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
PotentialNet for Molecular Property Prediction
Evan N. Feinberg et al.
ACS CENTRAL SCIENCE (2018)
Rigidity Strengthening: A Mechanism for Protein-Ligand Binding
Duc D. Nguyen et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction
Youjun Xu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions
Yang Li et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction
Connor W. Coley et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
Zixuan Cang et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies
Bao Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Forman curvature for complex networks
R. P. Sreejith et al.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2016)
Classification of Current Scoring Functions
Jie Liu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
Hongjian Li et al.
MOLECULAR INFORMATICS (2015)
PDB-wide collection of binding data: current status of the PDBbind database
Zhihai Liu et al.
BIOINFORMATICS (2015)
Open Babel: An open chemical toolbox
Noel M. O'Boyle et al.
JOURNAL OF CHEMINFORMATICS (2011)
Extended-Connectivity Fingerprints
David Rogers et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
Ricci curvature for metric-measure spaces via optimal transport
John Lott et al.
ANNALS OF MATHEMATICS (2009)
Mass transportation and rough curvature bounds for discrete spaces
Anca-Iuliana Bonciocat et al.
JOURNAL OF FUNCTIONAL ANALYSIS (2009)
Ricci curvature of Markov chains on metric spaces
Yann Ollivier
JOURNAL OF FUNCTIONAL ANALYSIS (2009)
Ricci curvature of metric spaces
Yann Ollivier
COMPTES RENDUS MATHEMATIQUE (2007)
ErG: 2D pharmacophore descriptions for scaffold hopping
N Stiefl et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
Computing persistent homology
A Zomorodian et al.
DISCRETE & COMPUTATIONAL GEOMETRY (2005)
Automatic generation of complementary descriptors with molecular graph networks
C Merkwirth et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2005)
Bochner's method for cell complexes and combinatorial Ricci curvature
R Forman
DISCRETE & COMPUTATIONAL GEOMETRY (2003)
Topological persistence and simplification
H Edelsbrunner et al.
DISCRETE & COMPUTATIONAL GEOMETRY (2002)
Reoptimization of MDL keys for use in drug discovery
JL Durant et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2002)
Share Paper
