Assessing the potential of deep learning for protein-ligand docking
Fuente:
arXiv
Saved in:
| Main Authors: | Morehead, Alex, Giri, Nabin, Liu, Jian, Neupane, Pawan, Cheng, Jianlin |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization
by: Morehead, Alex, et al.
Published: (2023)
by: Morehead, Alex, et al.
Published: (2023)
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
by: Morehead, Alex, et al.
Published: (2024)
by: Morehead, Alex, et al.
Published: (2024)
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
by: Morehead, Alex, et al.
Published: (2023)
by: Morehead, Alex, et al.
Published: (2023)
Learning Inter-Atomic Potentials without Explicit Equivariance
by: Elhag, Ahmed A., et al.
Published: (2025)
by: Elhag, Ahmed A., et al.
Published: (2025)
Protein Folding with Neural Ordinary Differential Equations
by: Sanford, Arielle, et al.
Published: (2025)
by: Sanford, Arielle, et al.
Published: (2025)
Autoregressive fragment-based diffusion for pocket-aware ligand design
by: Ghorbani, Mahdi, et al.
Published: (2023)
by: Ghorbani, Mahdi, et al.
Published: (2023)
AgenticPosesRanker: An Agentic AI Framework for Physically Grounded Ranking of Protein-Ligand Docking Poses
by: Khiari, Sofiene, et al.
Published: (2026)
by: Khiari, Sofiene, et al.
Published: (2026)
An AI Implementation Science Study to Improve Trustworthy Data in a Large Healthcare System
by: Marteau, Benoit L., et al.
Published: (2025)
by: Marteau, Benoit L., et al.
Published: (2025)
Dynamic optimization of volatile fatty acids to enrich biohydrogen production using a deep learning neural network
by: Mahmoodi-Eshkaftaki, Mahmood, et al.
Published: (2022)
by: Mahmoodi-Eshkaftaki, Mahmood, et al.
Published: (2022)
LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
by: Phan, An, et al.
Published: (2026)
by: Phan, An, et al.
Published: (2026)
Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
by: Baillif, Benoit, et al.
Published: (2024)
by: Baillif, Benoit, et al.
Published: (2024)
Quantification of protein homodimer affinity using native mass spectrometry
by: Schulte, Jonathan, et al.
Published: (2025)
by: Schulte, Jonathan, et al.
Published: (2025)
gRNAde: Geometric Deep Learning for 3D RNA inverse design
by: Joshi, Chaitanya K., et al.
Published: (2023)
by: Joshi, Chaitanya K., et al.
Published: (2023)
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction
by: Schapin, Nikolai, et al.
Published: (2024)
by: Schapin, Nikolai, et al.
Published: (2024)
Combining oligo pools and Golden Gate cloning to create protein variant libraries or guide RNA libraries for CRISPR applications
by: Valero, Alicia Maciá, et al.
Published: (2024)
by: Valero, Alicia Maciá, et al.
Published: (2024)
Canonicalization of the E value from BLAST similarity search -- dissimilarity measure and distance function for a metric space of protein sequences
by: Mao, Boryeu
Published: (2025)
by: Mao, Boryeu
Published: (2025)
Improved Cryo-EM Pose Estimation and 3D Classification through Latent-Space Disentanglement
by: Chen, Weijie, et al.
Published: (2023)
by: Chen, Weijie, et al.
Published: (2023)
Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation
by: Wee, JunJie, et al.
Published: (2024)
by: Wee, JunJie, et al.
Published: (2024)
Accurate RNA 3D structure prediction using a language model-based deep learning approach
by: Shen, Tao, et al.
Published: (2022)
by: Shen, Tao, et al.
Published: (2022)
Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning
by: Wee, JunJie, et al.
Published: (2024)
by: Wee, JunJie, et al.
Published: (2024)
ApisTox: a new benchmark dataset for the classification of small molecules toxicity on honey bees
by: Adamczyk, Jakub, et al.
Published: (2024)
by: Adamczyk, Jakub, et al.
Published: (2024)
AI-predicted protein deformation encodes energy landscape
by: Mcbride, John M, et al.
Published: (2023)
by: Mcbride, John M, et al.
Published: (2023)
Exploring zero-shot structure-based protein fitness prediction
by: Sharma, Arnav, et al.
Published: (2025)
by: Sharma, Arnav, et al.
Published: (2025)
Protein folding classes -- High-dimensional geometry of amino acid composition space revisited
by: Mao, Boryeu
Published: (2025)
by: Mao, Boryeu
Published: (2025)
GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
by: Lindsey, Michael
Published: (2026)
by: Lindsey, Michael
Published: (2026)
Explainable Machine Learning and Deep Learning Models for Predicting TAS2R-Bitter Molecule Interactions
by: Ferri, Francesco, et al.
Published: (2024)
by: Ferri, Francesco, et al.
Published: (2024)
Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
by: Reilly, Charles B
Published: (2026)
by: Reilly, Charles B
Published: (2026)
AntiFold: Improved antibody structure-based design using inverse folding
by: Høie, Magnus Haraldson, et al.
Published: (2024)
by: Høie, Magnus Haraldson, et al.
Published: (2024)
HelixVS: Deep Learning-Enhanced Structure-Based Platform for Screening and Design
by: Zhang, Shanzhuo, et al.
Published: (2025)
by: Zhang, Shanzhuo, et al.
Published: (2025)
EscalNet: Learn isotropic representation space for biomolecular dynamics based on effective energy
by: Zuo, Guanghong
Published: (2025)
by: Zuo, Guanghong
Published: (2025)
Network Pharmacology Framework Characterizes Polypharmacological Properties of Dietary Flavonoids: Integration of Computational, Experimental, and Epidemiological Evidence
by: Fujisaki, Koyo, et al.
Published: (2026)
by: Fujisaki, Koyo, et al.
Published: (2026)
Persistent Sheaf Laplacian Analysis of Protein Flexibility
by: Hayes, Nicole, et al.
Published: (2025)
by: Hayes, Nicole, et al.
Published: (2025)
Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases
by: Di Gregorio, Elisabetta, et al.
Published: (2023)
by: Di Gregorio, Elisabetta, et al.
Published: (2023)
mRNA Folding Algorithms for Structure and Codon Optimization
by: Ward, Max, et al.
Published: (2025)
by: Ward, Max, et al.
Published: (2025)
Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
by: Clark, Joseph D., et al.
Published: (2025)
by: Clark, Joseph D., et al.
Published: (2025)
Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited
by: Tsampazi, Vasiliki, et al.
Published: (2026)
by: Tsampazi, Vasiliki, et al.
Published: (2026)
Predicting Protein-Nucleic Acid Flexibility Using Persistent Sheaf Laplacians
by: Hayes, Nicole, et al.
Published: (2025)
by: Hayes, Nicole, et al.
Published: (2025)
Conformational landscapes in cryo-ET data based on MD simulations
by: Jonic, Slavica
Published: (2026)
by: Jonic, Slavica
Published: (2026)
Non-perturbative Bacterial Identification Directly from Solid Agar Plates Using Raman
by: Kim, Jeong Hee, et al.
Published: (2026)
by: Kim, Jeong Hee, et al.
Published: (2026)
VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels
by: Wang, Rui, et al.
Published: (2026)
by: Wang, Rui, et al.
Published: (2026)
Similar Items
-
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization
by: Morehead, Alex, et al.
Published: (2023) -
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
by: Morehead, Alex, et al.
Published: (2024) -
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
by: Morehead, Alex, et al.
Published: (2023) -
Learning Inter-Atomic Potentials without Explicit Equivariance
by: Elhag, Ahmed A., et al.
Published: (2025) -
Protein Folding with Neural Ordinary Differential Equations
by: Sanford, Arielle, et al.
Published: (2025)