GitHub Repositories
Software developed and maintained by the Lin Research Group for molecular modeling, biomolecular interactions, RNA folding, structure refinement, nucleosome and chromatin simulation, and R-loop benchmarking.
Protein-DNA binding
IDEA_Model
Interpretable protein-DNA Energy Associative model for learning physicochemical interactions from structures and sequences.
Protein-RNA affinity
IRIS_Model
Integrative RNA-protein interaction prediction informed by structure and sequence, with workflows for model training and binding-energy prediction.
Methylated DNA binding
mIDEA_Model
Methylation-informed IDEA model for predicting and interpreting methylation-dependent protein-DNA binding specificity.
RNA folding simulation
SSPN_RNA_Model
RNA modeling capabilities for a single-site-per-nucleotide model, implemented as a modification to OpenABC with tutorial examples.
R-loop prediction
RLoopBench
Benchmarking suite for R-loop prediction methods across datasets, species, and model classes.
T cell specificity
RACER
Rapid assessment framework for sparse T cell receptor specificity prediction using structural features.
Protein structure refinement
PC-guided_protein_structure_refinement
Principal-component-guided workflow for protein structure prediction and refinement.
Chromatin simulation
Explicit-ion Chromatin Model
Explicit-ion modeling resources for physicochemical interactions in chromatin organization.
Nucleosome simulation
OpenABC_nucl
OpenABC-based modeling resources for nucleosome systems and chromatin-related molecular simulations.