COLOR

COLOR: A Compositional Linear Operation-Based Representation of Protein Sequences for Identification of Monomer Contributions to Properties.

2025.12.0300

iPiDA_CL

Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods.

2025.12.0300

TransABseq

TransABseq: A Two-Stage Approach for Predicting Antigen-Antibody Binding Affinity Changes upon Mutation Based on Protein Sequences.

2025.12.0300

COBY

Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems.

2025.12.0300

AbSet

AbSet: A Standardized Data Set of Antibody Structures for Machine Learning Applications.

2025.12.0300

DrugEx

Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design.

2025.12.0300

MolSnapper

MolSnapper: Conditioning Diffusion for Structure-Based Drug Design.

2025.12.0300

CMD-FGKpuu

Predicting the Brain-To-Plasma Unbound Partition Coefficient of Compounds via Formula-Guided Network.

2025.12.0300

MTPSol

MTPSol: Multimodal Twin Protein Solubility Prediction Architecture Based on Pretrained Models.

2025.12.0300

CycDockAssem

De Novo Design of Cyclic Peptide Binders Based on Fragment Docking and Assembling.

2025.12.0300

MVDSA

Multi-Knowledge Graph and Multi-View Entity Feature Learning for Predicting Drug-Related Side Effects.

2025.12.0300

MHNfs

MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery.

2025.12.0300

wall-EASAL

A New Discrete-Geometry Approach for Integrative Docking of Proteins Using Chemical Cross-Links.

2025.12.0300

PyPE_RESP

PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges.

2025.12.0300

DCGHCN

Utilizing Dual-Channel Graph and Hypergraph Convolution Network to Discover Microbes Underlying Disease Traits.

2025.12.0300

gnn-descriptor

Advancements in Ligand-Based Virtual Screening through the Synergistic Integration of Graph Neural Networks and Expert-Crafted Descriptors.

2025.12.0300

HGCL-DR

Heterogeneous Graph Contrastive Learning with Graph Diffusion for Drug Repositioning.

2025.12.0300

Vina-CUDA

Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking.

2025.12.0300

CrypToth

CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.

2025.12.0300

FE-ToolKit

FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.

2025.12.0300

ChemXploreML

Machine Learning Pipeline for Molecular Property Prediction Using ChemXploreML.

2025.12.0300

LLM-MPP

Effective and Explainable Molecular Property Prediction by Chain-of-Thought Enabled Large Language Models and Multi-Modal Molecular Information Fusion.

2025.12.0300

DLST-MDA

Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA-Drug Associations.

2025.12.0300

OpHReda

Advancing Enzyme Optimal pH Prediction via Retrieved Embedding Data Augmentation.

2025.12.0300

OxPot

Predicting Oxidation Potentials with DFT-Driven Machine Learning.

2025.12.0300

GICL

GICL: A Cross-Modal Drug Property Prediction Framework Based on Knowledge Enhancement of Large Language Models.

2025.12.0300

MGCA

Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction.

2025.12.0300

GArNet

GArNet: A Genetic Algorithm-Based Protein Redesign Approach to Optimize Mutation Combinations Informed by Network Theory.

2025.12.0300

EMMPTNet

Explainable RNA-Small Molecule Binding Affinity Prediction Based on Multiview Enhancement Learning.

2025.12.0300

pylambdaopt

Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy Calculations.

2025.12.0300

PySSA

PySSA for Windows: End-User Protein Structure Prediction and Visual Analysis with ColabFold and PyMOL.

2025.12.0300

RosettaAMRLD

RosettaAMRLD: A Reaction-Driven Approach for Structure-Based Drug Design from Combinatorial Libraries with Monte Carlo Metropolis Algorithms.

2025.12.0300

HX-ESP

Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.

2025.12.0300

CycleDesigner

CycleDesigner: Leveraging CycRFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets.

2025.12.0300

AVP-HNCL

AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction.

2025.12.0300

MTGNN

MTGNN: A Drug-Target-Disease Triplet Association Prediction Model Based on Multimodal Heterogeneous Graph Neural Networks and Direction-Aware Metapaths.

2025.12.0300

MlCOFSyn

MlCOFSyn: A Machine Learning Framework To Facilitate the Synthesis of 2D Covalent Organic Frameworks.

2025.12.0300

MOFF

Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments.

2025.12.0300

RIdiffusion

A Hyperbolic Discrete Diffusion 3D RNA Inverse Folding Model for Functional RNA Design.

2025.12.0300

DrugBaiter

Improved Prediction of Drug-Protein Interactions through Physics-Based Few-Shot Learning.

2025.12.0300