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

ESES: Software for Eulerian solvent excluded surface

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

Documentation of an Imperative To Improve Methods for Predicting Membrane Protein Stability

(2016) Brett M. Kroncke et al.   BIOCHEMISTRY

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach

(2016) Ivan Getov et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies

(2016) Bao Wang et al.   JOURNAL OF CHEMICAL PHYSICS

The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling

(2016) Duc D. Nguyen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Object-oriented persistent homology

(2016) Bao Wang et al.   JOURNAL OF COMPUTATIONAL PHYSICS

EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models

(2016) Lukas Folkman et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins

(2015) Tugba G Kucukkal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Multiresolution persistent homology for excessively large biomolecular datasets

(2015) Kelin Xia et al.   JOURNAL OF CHEMICAL PHYSICS

Multidimensional persistence in biomolecular data

(2015) Kelin Xia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2014) Zhihai Liu et al.   BIOINFORMATICS

Persistent homology analysis of protein structure, flexibility, and folding

(2014) Kelin Xia et al.   International Journal for Numerical Methods in Biomedical Engineering

A topological measurement of protein compressibility

(2014) Marcio Gameiro et al.   JAPAN JOURNAL OF INDUSTRIAL AND APPLIED MATHEMATICS

Persistent homology for the quantitative prediction of fullerene stability

(2014) Kelin Xia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

(2014) Niklas Berliner et al.   PLoS One

Determining the topology of stable protein–DNA complexes

(2013) Isabel K. Darcy et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Morse Theory for Filtrations and Efficient Computation of Persistent Homology

(2013) Konstantin Mischaikow et al.   DISCRETE & COMPUTATIONAL GEOMETRY

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

The Movable Type Method Applied to Protein–Ligand Binding

(2013) Zheng Zheng et al.   Journal of Chemical Theory and Computation

Structure-based prediction of the effects of a missense variant on protein stability

(2012) Yang Yang et al.   AMINO ACIDS

Analyzing Effects of Naturally Occurring Missense Mutations

(2012) Zhe Zhang et al.   Computational and Mathematical Methods in Medicine

A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction

(2012) Hossam M. Ashtawy et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

(2012) Xin Feng et al.   International Journal for Numerical Methods in Biomedical Engineering

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology

(2012) Y. Dabaghian et al.   PLoS Computational Biology

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Persistent Cohomology and Circular Coordinates

(2011) Vin de Silva et al.   DISCRETE & COMPUTATIONAL GEOMETRY

Ligand Identification Scoring Algorithm (LISA)

(2011) Zheng Zheng et al.   Journal of Chemical Information and Modeling

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

(2011) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Persistent Intersection Homology

(2010) Paul Bendich et al.   FOUNDATIONS OF COMPUTATIONAL MATHEMATICS

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

The Theory of Multidimensional Persistence

(2009) Gunnar Carlsson et al.   DISCRETE & COMPUTATIONAL GEOMETRY

Structure-Based Predictive Models for Allosteric Hot Spots

(2009) Omar N. A. Demerdash et al.   PLoS Computational Biology

Extending Persistence Using Poincaré and Lefschetz Duality

(2008) David Cohen-Steiner et al.   FOUNDATIONS OF COMPUTATIONAL MATHEMATICS

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

(2008) Shuangye Yin et al.   Journal of Chemical Information and Modeling