Research topics:

• To use computational tools from PDE, differential geometry, algebraic topology and statistical learning to study the biomolecular structure, flexibility, dynamics, and functions.
• Topological data analysis (TDA), topology based machine learning/deep learning models, and their applications in drug design.

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11 to 20 of 69 Results
Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions
Jun 23, 2023
Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions", https://doi.org/10.21979/N9/ZTA5MN, DR-NTU (Data), V1
Artificial intelligence (AI) techniques have already been gradually applied to the entire drug design process, from target discovery, lead discovery, lead optimization and preclinical development to the final three phases of clinical trials. Currently, one of the central challeng...
Forman-Persistent-Ricci-Curvature.rar
Jun 23, 2023 - Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions
RAR Archive - 2.4 MB - MD5: 4226d6f100d5c4f2caab6009a454412a
Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules
Jun 12, 2023
Xia, Kelin, 2023, "Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules", https://doi.org/10.21979/N9/FIFOZS, DR-NTU (Data), V1
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules. The multiscale virtual particle (MVP) model is proposed for the discretization of biomolecular density data. With this model, l...
VAULT_4V60_v1.rar
Jun 12, 2023 - Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules
RAR Archive - 45.3 MB - MD5: 11f50820eece6bfbe0058cb031c231d4
Data and Code for generating density profile of PDBID: 4V60
Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
Jun 12, 2023
Anand, D Vijay; Meng, Zhenyu; Xia, Kelin; Mu, Yuguang, 2023, "Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis", https://doi.org/10.21979/N9/IXD1QX, DR-NTU (Data), V1
It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanis...
WPH_Osmolytes.rar
Jun 12, 2023 - Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
RAR Archive - 16.9 KB - MD5: c7344a5c72aedc2ed88cef53fd39d358
Data and codes to replicate the weighted persistent homology for TMAO and urea.
Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design
Apr 6, 2021
Xia, Kelin, 2021, "Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design", https://doi.org/10.21979/N9/16CFBW, DR-NTU (Data), V2
Artificial intelligence (AI) based drug design has demonstrated great potential to fundamentally change the pharmaceutical industries. Currently, a key issue in AI-based drug design is efficient transferable molecular descriptors or fingerprints. Here, we present hypergraph-based...
Hypergraph-based-Persistent-Cohomology-master.zip
Apr 6, 2021 - Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design
ZIP Archive - 185.3 MB - MD5: 38015fd58aee816e3cc070e48f1fe80d
Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction
Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction
Apr 2, 2021
Xia, Kelin, 2021, "Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction", https://doi.org/10.21979/N9/JHXLSG, DR-NTU (Data), V1
Efficient molecular featurization is one of the major issues for machine learning models in drug design. Here, we propose a persistent Ricci curvature (PRC), in particular, Ollivier PRC (OPRC), for the molecular featurization and feature engineering, for the first time. The filtr...
build_lig_2007.py
Apr 2, 2021 - Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction
Python Source Code - 4.9 KB - MD5: a7fc5e0fe3e67110c6ca3b80a0a667b4
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