Modeling and simulation of ion channels
C Maffeo, S Bhattacharya, J Yoo, D Wells… - Chemical …, 2012 - ACS Publications
Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …
A review of mathematical representations of biomolecular data
Recently, machine learning (ML) has established itself in various worldwide benchmarking
competitions in computational biology, including Critical Assessment of Structure Prediction …
competitions in computational biology, including Critical Assessment of Structure Prediction …
MathDL: mathematical deep learning for D3R Grand Challenge 4
We present the performances of our mathematical deep learning (MathDL) models for D3R
Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free …
Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free …
A topological approach for protein classification
Protein function and dynamics are closely related to its sequence and structure. However,
prediction of protein function and dynamics from its sequence and structure is still a …
prediction of protein function and dynamics from its sequence and structure is still a …
Variational multiscale models for charge transport
This work presents a few variational multiscale models for charge transport in complex
physical, chemical, and biological systems and engineering devices, such as fuel cells, solar …
physical, chemical, and biological systems and engineering devices, such as fuel cells, solar …
DG‐GL: Differential geometry‐based geometric learning of molecular datasets
Motivation: Despite its great success in various physical modeling, differential geometry
(DG) has rarely been devised as a versatile tool for analyzing large, diverse, and complex …
(DG) has rarely been devised as a versatile tool for analyzing large, diverse, and complex …
Multiscale multiphysics and multidomain models—Flexibility and rigidity
The emerging complexity of large macromolecules has led to challenges in their full scale
theoretical description and computer simulation. Multiscale multiphysics and multidomain …
theoretical description and computer simulation. Multiscale multiphysics and multidomain …
EISA-Score: Element Interactive Surface Area score for protein–ligand binding affinity prediction
Molecular surface representations have been advertised as a great tool to study protein
structure and functions, including protein–ligand binding affinity modeling. However, the …
structure and functions, including protein–ligand binding affinity modeling. However, the …
Object-oriented persistent homology
Persistent homology provides a new approach for the topological simplification of big data
via measuring the life time of intrinsic topological features in a filtration process and has …
via measuring the life time of intrinsic topological features in a filtration process and has …
Eses: Software for e ulerian solvent excluded surface
Solvent excluded surface (SES) is one of the most popular surface definitions in biophysics
and molecular biology. In addition to its usage in biomolecular visualization, it has been …
and molecular biology. In addition to its usage in biomolecular visualization, it has been …