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Assessment of protein–ligand complexes in CASP15

https://doi.org/10.1002/prot.26601
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/prot.10393openalex-snapshot
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
inferredcites →https://doi.org/10.1002/prot.26515openalex-snapshot
New prediction categories in CASP15
inferredcites →https://doi.org/10.1007/s10822-016-9946-8openalex-snapshot
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
inferredcites →https://doi.org/10.1007/s10822-017-0088-4openalex-snapshot
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
inferredcites →https://doi.org/10.1007/s10822-018-0180-4openalex-snapshot
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
inferredcites →https://doi.org/10.1007/s10822-019-00203-1openalex-snapshot
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen
inferredcites →https://doi.org/10.1007/s10822-020-00277-2openalex-snapshot
Conformational analysis of macrocycles: comparing general and specialized methods
inferredcites →https://doi.org/10.1007/s10822-020-00289-yopenalex-snapshot
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
inferredcites →https://doi.org/10.1016/j.jmgm.2012.07.007openalex-snapshot
Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases
inferredcites →https://doi.org/10.1016/j.str.2019.05.012openalex-snapshot
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
inferredcites →https://doi.org/10.1021/acs.jcim.5b00387openalex-snapshot
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
inferredcites →https://doi.org/10.1021/ci00007a012openalex-snapshot
Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited
inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
inferredcites →https://doi.org/10.1021/ci00062a008openalex-snapshot
SMILES. 2. Algorithm for generation of unique SMILES notation
inferredcites →https://doi.org/10.1021/ci400025fopenalex-snapshot
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1093/bioinformatics/btt473openalex-snapshot
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
inferredcites →https://doi.org/10.1107/s0907444913007051openalex-snapshot
OpenStructure: an integrated software framework for computational structural biology
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1186/s12859-019-3019-7openalex-snapshot
HH-suite3 for fast remote homology detection and deep protein annotation
inferredcites →https://doi.org/10.1186/s13321-020-00455-2openalex-snapshot
spyrmsd: symmetry-corrected RMSD calculations in Python
inferredcites →https://doi.org/10.25080/tcwv9851openalex-snapshot
Exploring Network Structure, Dynamics, and Function using NetworkX
inferredcites →https://doi.org/10.52202/068431-0525openalex-snapshot
TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/2211-5463.13902openalex-snapshot
An outlook on structural biology after A lpha F old: tools, limits and perspectives
inferred← citeshttps://doi.org/10.1002/prot.26515openalex-snapshot
New prediction categories in CASP15
inferred← citeshttps://doi.org/10.1002/prot.26605openalex-snapshot
Automated benchmarking of combined protein structure and ligand conformation prediction
inferred← citeshttps://doi.org/10.1002/prot.26617openalex-snapshot
Critical assessment of methods of protein structure prediction ( CASP )—Round XV
inferred← citeshttps://doi.org/10.1002/prot.26827openalex-snapshot
Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching
inferred← citeshttps://doi.org/10.1002/prot.70032openalex-snapshot
Ligand Binding Prediction on Pharmaceutical and Nucleic Acid Targets by the CoDock Group in CASP16
inferred← citeshttps://doi.org/10.1002/prot.70042openalex-snapshot
Updates to the CASP Infrastructure in 2024
inferred← citeshttps://doi.org/10.1002/prot.70060openalex-snapshot
Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn ( CAMEO )
inferred← citeshttps://doi.org/10.1002/prot.70061openalex-snapshot
Assessment of Pharmaceutical Protein–Ligand Pose and Affinity Predictions in CASP16
inferred← citeshttps://doi.org/10.1002/prot.70063openalex-snapshot
Protein–Ligand Structure Prediction by Template‐Guided Ensemble Docking Strategy
inferred← citeshttps://doi.org/10.1002/prot.70066openalex-snapshot
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16
inferred← citeshttps://doi.org/10.1002/prot.70072openalex-snapshot
Assessment of Nucleic Acid Structure Prediction in CASP16
inferred← citeshttps://doi.org/10.1002/prot.70079openalex-snapshot
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16
inferred← citeshttps://doi.org/10.1016/j.bpj.2026.04.011openalex-snapshot
Docking-based virtual screening: Past, present, and future
inferred← citeshttps://doi.org/10.1016/j.csbj.2025.07.028openalex-snapshot
Exploration of structural space of Cus17 lectin with glycans using molecular docking and simulation studies
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01170openalex-snapshot
A High-Quality Data Set of Protein–Ligand Binding Interactions Via Comparative Complex Structure Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00669openalex-snapshot
Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01860openalex-snapshot
Benchmarking Cofolding Methods for Molecular Glue Ternary Structure Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01985openalex-snapshot
TEMPL: A Template-Based Protein–Ligand Pose Prediction Baseline
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02777openalex-snapshot
ArtiDock: Accurate Machine Learning Approach to Protein–Ligand Docking Optimized for High-Throughput Virtual Screening
inferred← citeshttps://doi.org/10.1038/s41467-025-67127-3openalex-snapshot
Benchmarking all-atom biomolecular structure prediction with FoldBench
inferred← citeshttps://doi.org/10.1038/s41592-025-02973-zopenalex-snapshot
A fully automated benchmarking suite to compare macromolecular complexes
inferred← citeshttps://doi.org/10.1038/s41594-026-01797-5openalex-snapshot
Evaluating generalization in protein–ligand cofolding methods
inferred← citeshttps://doi.org/10.1038/s42003-024-07113-5openalex-snapshot
The Nobel Prize in Chemistry: past, present, and future of AI in biology
inferred← citeshttps://doi.org/10.1038/s42256-025-01160-1openalex-snapshot
Assessing the potential of deep learning for protein–ligand docking
inferred← citeshttps://doi.org/10.1093/glycob/cwae087openalex-snapshot
The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode
inferred← citeshttps://doi.org/10.1093/nar/gkae270openalex-snapshot
The structure assessment web server: for proteins, complexes and more
inferred← citeshttps://doi.org/10.1093/nar/gkaf391openalex-snapshot
E3Docker: a docking server for potential E3 binder discovery
inferred← citeshttps://doi.org/10.1101/2023.12.17.572051openalex-snapshot
Fully flexible molecular alignment enables accurate ligand structure modelling
inferred← citeshttps://doi.org/10.1101/2024.07.17.603955openalex-snapshot
PLINDER: The protein-ligand interactions dataset and evaluation resource
inferred← citeshttps://doi.org/10.1101/2024.11.19.624167openalex-snapshot
Boltz-1 Democratizing Biomolecular Interaction Modeling
inferred← citeshttps://doi.org/10.1101/2025.02.03.636309openalex-snapshot
Have protein-ligand cofolding methods moved beyond memorisation?
inferred← citeshttps://doi.org/10.1101/2025.05.25.655997openalex-snapshot
Comparative assessment of co-folding methods for molecular glue ternary structure prediction
inferred← citeshttps://doi.org/10.1186/s13321-025-01011-6openalex-snapshot
Assessing interaction recovery of predicted protein-ligand poses
inferred← citeshttps://doi.org/10.1186/s13321-025-01019-yopenalex-snapshot
Leveraging AI to explore structural contexts of post-translational modifications in drug binding
inferred← citeshttps://doi.org/10.3389/fphar.2024.1411428openalex-snapshot
Toward high-resolution modeling of small molecule–ion channel interactions
inferred← citeshttps://doi.org/10.3389/frbis.2026.1937302openalex-snapshot
Benchmarking protein-ligand co-folding across Nav, Cav and Kv-family channels
inferred← citeshttps://doi.org/10.3390/md22050206openalex-snapshot
Anti-Melanogenic Effects of Takifugu flavidus Muscle Hydrolysate in B16F10 Melanoma Cells and Zebrafish
inferred← citeshttps://doi.org/10.3390/molecules29040832openalex-snapshot
Recent Progress of Protein Tertiary Structure Prediction
inferred← citeshttps://doi.org/10.64898/2025.12.09.693161openalex-snapshot
Comparative Assessment of the Utility of Co-Folding and Docking for Small-Molecule Drug Design
inferred← citeshttps://doi.org/10.64898/2025.12.30.696741openalex-snapshot
Bento: Benchmarking Classical and AI Docking on Drug Design–Relevant Data
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A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction
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