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Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies
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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.20084openalex-snapshot
UCSF Chimera—A visualization system for exploratory research and analysis
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/10.1007/s10822-016-9946-8openalex-snapshot
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
inferredcites →https://doi.org/10.1007/s10822-017-0038-1openalex-snapshot
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015
inferredcites →https://doi.org/10.1007/s10822-017-0082-xopenalex-snapshot
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor
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/s10822-019-00185-0openalex-snapshot
Predicting protein–ligand binding modes for CELPP and GC3: workflows and insight
inferredcites →https://doi.org/10.1007/s10822-019-00237-5openalex-snapshot
MathDL: mathematical deep learning for D3R Grand Challenge 4
inferredcites →https://doi.org/10.1007/s10822-019-00257-1openalex-snapshot
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
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/10.1007/s41048-017-0045-8openalex-snapshot
Docking-based inverse virtual screening: methods, applications, and challenges
inferredcites →https://doi.org/10.1016/j.sbi.2023.102548openalex-snapshot
Structure-based drug design with geometric deep learning
inferredcites →https://doi.org/10.1021/acs.jcim.2c00485openalex-snapshot
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions
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/acs.jcim.5b00504openalex-snapshot
Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks
inferredcites →https://doi.org/10.1021/acs.jcim.5b00523openalex-snapshot
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
inferredcites →https://doi.org/10.1021/ci100031xopenalex-snapshot
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci200060sopenalex-snapshot
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening
inferredcites →https://doi.org/10.1021/ci2000727openalex-snapshot
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function
inferredcites →https://doi.org/10.1021/ci200269qopenalex-snapshot
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
inferredcites →https://doi.org/10.1021/ci300314kopenalex-snapshot
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
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/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/s41586-021-03819-2openalex-snapshot
Highly accurate protein structure prediction with AlphaFold
inferredcites →https://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
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/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferredcites →https://doi.org/10.3390/ijms222212320openalex-snapshot
Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies
inferredcites →https://doi.org/10.3390/molecules190710150openalex-snapshot
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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.70063openalex-snapshot
Protein–Ligand Structure Prediction by Template‐Guided Ensemble Docking Strategy
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.carres.2024.109022openalex-snapshot
How alginate lyase produces quasi-monodisperse oligosaccharides: A normal-mode-based docking and molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00669openalex-snapshot
Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling
inferred← citeshttps://doi.org/10.1093/nar/gkag417openalex-snapshot
CB-Dock3: an enhanced web server for protein–ligand blind docking
inferred← citeshttps://doi.org/10.1101/2023.12.17.572051openalex-snapshot
Fully flexible molecular alignment enables accurate ligand structure modelling
inferred← citeshttps://doi.org/10.20944/preprints202404.0576.v1openalex-snapshot
A Reversible Spherical Geometric Conversion of Protein Backbone Structure Coordinate Matrix to Three Independent Vectors of ρ, θ and φ
inferred← citeshttps://doi.org/10.2174/0115748936285690240101041704openalex-snapshot
Advances in Deep Learning Assisted Drug Discovery Methods: A Self-review
inferred← citeshttps://doi.org/10.3390/molecules29040832openalex-snapshot
Recent Progress of Protein Tertiary Structure Prediction
inferred← citeshttps://doi.org/10.4310/cis.241021221101openalex-snapshot
Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design
inferred← citeshttps://doi.org/10.64659/jomi/211255openalex-snapshot
MODELLER-Based Homology Modeling: A Critical Review of Protocols, Advances, and Computational Challenges
inferred← citeshttps://doi.org/10.70675/e211ffb4z6d6fz476ez9441z34c4cdf8d79aopenalex-snapshot
Fragment-based modelling of protein-RNA complexes for protein design
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