MLIMC: Machine learning-based implicit-solvent Monte Carlo

Combining the Fragmentation Approach and Neural Network Potential Energy Surfaces of Fragments for Accurate Calculation of Protein Energy

(2020) Zhilong Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

(2019) Huali Cao et al.   Journal of Chemical Information and Modeling

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

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

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

(2018) David Bramer et al.   JOURNAL OF CHEMICAL PHYSICS

TopP -S : Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility

(2018) Kedi Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

A neural network potential energy surface for the F + CH4 reaction including multiple channels based on coupled cluster theory

(2018) Jun Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2018) Zixuan Cang et al.   PLoS Computational Biology

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

(2018) Duc Duy Nguyen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

(2017) Negin Forouzesh et al.   Journal of Chemical Information and Modeling

Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies

(2017) Duc D. Nguyen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

ESES: Software for Eulerian solvent excluded surface

(2017) Beibei Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A two-component Matched Interface and Boundary (MIB) regularization for charge singularity in implicit solvation

(2017) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets

(2017) Alexandru Korotcov et al.   MOLECULAR PHARMACEUTICS

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

(2015) Tyler B. Hughes et al.   ACS Central Science

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

(2014) Zhihai Liu et al.   BIOINFORMATICS

AFMPB: An adaptive fast multipole Poisson–Boltzmann solver for calculating electrostatics in biomolecular systems

(2013) Benzhuo Lu et al.   COMPUTER PHYSICS COMMUNICATIONS

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

A treecode-accelerated boundary integral Poisson–Boltzmann solver for electrostatics of solvated biomolecules

(2013) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

(2013) Sergio Decherchi et al.   PLoS One

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

Multiscale molecular dynamics using the matched interface and boundary method

(2010) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

(2008) Sunhwan Jo et al.   NUCLEIC ACIDS RESEARCH