Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction

Machine‐learning scoring functions for structure‐based drug lead optimization

(2020) Hongjian Li et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Persistent spectral graph

(2020) Rui Wang et al.   International Journal for Numerical Methods in Biomedical Engineering

Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

(2020) D. Vijay Anand et al.   Scientific Reports

Community Detection on Networks with Ricci Flow

(2019) Chien-Chun Ni et al.   Scientific Reports

Ollivier-Ricci Curvature-Based Method to Community Detection in Complex Networks

(2019) Jayson Sia et al.   Scientific Reports

Advancing Drug Discovery via Artificial Intelligence

(2019) H.C. Stephen Chan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Network curvature as a hallmark of brain structural connectivity

(2019) Hamza Farooq et al.   Nature Communications

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Improving classical scoring functions using random forest: The non-additivity of free energy terms’ contributions in binding

(2018) Karim Afifi et al.   Chemical Biology & Drug Design

Machine learning in chemoinformatics and drug discovery

(2018) Yu-Chen Lo et al.   DRUG DISCOVERY TODAY

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks

(2018) Kedi Wu et al.   Journal of Chemical Information and Modeling

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Ollivier--Ricci Idleness Functions of Graphs

(2018) D. P. Bourne et al.   SIAM JOURNAL ON DISCRETE MATHEMATICS

Comparative analysis of two discretizations of Ricci curvature for complex networks

(2018) Areejit Samal et al.   Scientific Reports

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

(2018) Zixuan Cang et al.   PLoS Computational Biology

Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions

(2018) Maciej Wójcikowski et al.   BIOINFORMATICS

Artificial intelligence in drug development: present status and future prospects

(2018) Kit-Kay Mak et al.   DRUG DISCOVERY TODAY

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction

(2017) Zixuan Cang et al.   International Journal for Numerical Methods in Biomedical Engineering

Rigidity Strengthening: A Mechanism for Protein–Ligand Binding

(2017) Duc D. Nguyen et al.   Journal of Chemical Information and Modeling

AI-powered drug discovery captures pharma interest

(2017) Eric Smalley   NATURE BIOTECHNOLOGY

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

(2017) Zixuan Cang et al.   PLoS Computational Biology

Machine learning in materials informatics: recent applications and prospects

(2017) Rampi Ramprasad et al.   npj Computational Materials

Computer Aided Drug Design: Success and Limitations

(2016) Mohammad Hassan Baig et al.   CURRENT PHARMACEUTICAL DESIGN

Forman curvature for complex networks

(2016) R P Sreejith et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Trends in clinical success rates

(2016) Katarzyna Smietana et al.   NATURE REVIEWS DRUG DISCOVERY

The Next Era: Deep Learning in Pharmaceutical Research

(2016) Sean Ekins   PHARMACEUTICAL RESEARCH

Ricci curvature: An economic indicator for market fragility and systemic risk

(2016) R. S. Sandhu et al.   Science Advances

Role of computer-aided drug design in modern drug discovery

(2015) Stephani Joy Y. Macalino et al.   ARCHIVES OF PHARMACAL RESEARCH

Machine learning in computational docking

(2015) Mohamed A. Khamis et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints

(2015) Olexandr Isayev et al.   CHEMISTRY OF MATERIALS

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

(2015) Hongjian Li et al.   Molecular Informatics

Accelerated materials property predictions and design using motif-based fingerprints

(2015) Tran Doan Huan et al.   PHYSICAL REVIEW B

Graph Curvature for Differentiating Cancer Networks

(2015) Romeil Sandhu et al.   Scientific Reports

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

How to represent crystal structures for machine learning: Towards fast prediction of electronic properties

(2014) K. T. Schütt et al.   PHYSICAL REVIEW B

Ricci curvature and eigenvalue estimate on locally finite graphs

(2013) Yong Lin et al.   MATHEMATICAL RESEARCH LETTERS

Ricci curvature of graphs

(2012) Yong Lin et al.   TOHOKU MATHEMATICAL JOURNAL

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Ricci curvature for metric-measure spaces via optimal transport

(2009) John Lott et al.   ANNALS OF MATHEMATICS

Recent advances in computer-aided drug design

(2009) C. M. Song et al.   BRIEFINGS IN BIOINFORMATICS

Mass transportation and rough curvature bounds for discrete spaces

(2009) Anca-Iuliana Bonciocat et al.   JOURNAL OF FUNCTIONAL ANALYSIS

Ricci curvature of Markov chains on metric spaces

(2008) Yann Ollivier   JOURNAL OF FUNCTIONAL ANALYSIS