Weighted-persistent-homology-based machine learning for RNA flexibility analysis

Machine learning in chemoinformatics and drug discovery

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

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

(2018) Zixuan Cang et al.   PLoS Computational Biology

Blind prediction of protein B-factor and flexibility

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

Weighted persistent homology

(2018) Shiquan Ren et al.   ROCKY MOUNTAIN JOURNAL OF MATHEMATICS

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

B -factor profile prediction for RNA flexibility using support vector machines

(2017) Ivantha Guruge et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2017) Zixuan Cang et al.   PLoS Computational Biology

Efficient and robust persistent homology for measures

(2016) Mickaël Buchet et al.   COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Molecular nonlinear dynamics and protein thermal uncertainty quantification

(2014) Kelin Xia et al.   CHAOS

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

(2014) Kristopher Opron et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale multiphysics and multidomain models—Flexibility and rigidity

(2013) Kelin Xia et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic model for protein flexibility analysis

(2013) Kelin Xia et al.   PHYSICAL REVIEW E

Topological Strata of Weighted Complex Networks

(2013) Giovanni Petri et al.   PLoS One

Witnessed k-Distance

(2012) Leonidas Guibas et al.   DISCRETE & COMPUTATIONAL GEOMETRY

PredyFlexy: flexibility and local structure prediction from sequence

(2012) A. G. de Brevern et al.   NUCLEIC ACIDS RESEARCH

Robust Prediction of B-Factor Profile from Sequence Using Two-Stage SVR Based on Random Forest Feature Selection

(2009) Xiao-Yong Pan et al.   PROTEIN AND PEPTIDE LETTERS

Deriving protein dynamical properties from weighted protein contact number

(2008) Chih-Peng Lin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS