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MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

https://doi.org/10.1021/ci8001167
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What this work says

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

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Virtual screening and fast automated docking methods
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What points at this work

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

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Docking, Scoring, and Virtual Screening in Drug Discovery
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Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations
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Identification of Novel Integrin Binding Partners for Calcium and Integrin Binding Protein 1 (CIB1): Structural and Thermodynamic Basis of CIB1 Promiscuity
inferred← citeshttps://doi.org/10.1021/ci100218topenalex-snapshot
Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands
inferred← citeshttps://doi.org/10.1021/ci200146eopenalex-snapshot
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets
inferred← citeshttps://doi.org/10.1021/ci2002507openalex-snapshot
Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci200269qopenalex-snapshot
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci300478yopenalex-snapshot
Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark
inferred← citeshttps://doi.org/10.1021/ci400040dopenalex-snapshot
Docking Challenge: Protein Sampling and Molecular Docking Performance
inferred← citeshttps://doi.org/10.1021/ci400216qopenalex-snapshot
Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
inferred← citeshttps://doi.org/10.1021/ci5002026openalex-snapshot
Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2
inferred← citeshttps://doi.org/10.1021/ci500519wopenalex-snapshot
Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark
inferred← citeshttps://doi.org/10.1021/ci500731aopenalex-snapshot
Classification of Current Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci800313hopenalex-snapshot
Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case
inferred← citeshttps://doi.org/10.1021/ci9004139openalex-snapshot
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
inferred← citeshttps://doi.org/10.1021/ct300497zopenalex-snapshot
MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein–Protein Docking
inferred← citeshttps://doi.org/10.1021/es5038194openalex-snapshot
Structure–Function Relationship of PAMAM Dendrimers as Robust Oil Dispersants
inferred← citeshttps://doi.org/10.1038/s41375-025-02816-yopenalex-snapshot
Targeting IL-1/IRAK1/4 signaling in acute myeloid leukemia stem cells following treatment and relapse
inferred← citeshttps://doi.org/10.1038/s41598-017-02597-0openalex-snapshot
Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity
inferred← citeshttps://doi.org/10.1038/s44386-026-00063-4openalex-snapshot
Data driven selection of consensus docking pipelines for structure based hit identification
inferred← citeshttps://doi.org/10.1038/srep02273openalex-snapshot
Competitive Binding of Natural Amphiphiles with Graphene Derivatives
inferred← citeshttps://doi.org/10.1038/srep37175openalex-snapshot
Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins
inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
inferred← citeshttps://doi.org/10.1039/c4cp04996aopenalex-snapshot
Thermostability and reversibility of silver nanoparticle–protein binding
inferred← citeshttps://doi.org/10.1039/c8nr07180bopenalex-snapshot
Graphene quantum dots against human IAPP aggregation and toxicity in vivo
inferred← citeshttps://doi.org/10.1039/d0nr02710copenalex-snapshot
Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots
inferred← citeshttps://doi.org/10.1039/d1cp04246gopenalex-snapshot
Graphene quantum dots obstruct the membrane axis of Alzheimer's amyloid beta
inferred← citeshttps://doi.org/10.1039/d2cp02851dopenalex-snapshot
Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/d2cp04671gopenalex-snapshot
Hierarchical analysis of the target-based scoring function modification for the example of selected class A GPCRs
inferred← citeshttps://doi.org/10.1039/d3cp04138gopenalex-snapshot
Co-aggregation of α-synuclein with amyloid-β stabilizes β-sheet-rich oligomers and enhances the formation of β-barrels
inferred← citeshttps://doi.org/10.1039/d3sm01332dopenalex-snapshot
Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin
inferred← citeshttps://doi.org/10.1039/d4nr05075dopenalex-snapshot
Unveiling the inhibition mechanism of host-defense peptide cathelicidin LL-37 on the amyloid aggregation of the human islet amyloid polypeptide
inferred← citeshttps://doi.org/10.1039/d5nr03981aopenalex-snapshot
Molecular interaction modes of the host-defense peptide cathelicidin LL-37 and its mutants dictate diverse antimicrobial activities
inferred← citeshttps://doi.org/10.1063/1.5008874openalex-snapshot
High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers
inferred← citeshttps://doi.org/10.1063/1.5133601openalex-snapshot
Survey of the scoring functions for protein-ligand docking
inferred← citeshttps://doi.org/10.1074/jbc.m112.433789openalex-snapshot
Structural Determinants of Skeletal Muscle Ryanodine Receptor Gating*
inferred← citeshttps://doi.org/10.1080/07391102.2021.1971558openalex-snapshot
Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation
inferred← citeshttps://doi.org/10.1088/2632-2153/ae29bcopenalex-snapshot
CAP: Commutative algebra prediction of protein-nucleic acid binding affinities
inferred← citeshttps://doi.org/10.1093/bib/bbad192openalex-snapshot
emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model
inferred← citeshttps://doi.org/10.1093/bib/bbad526openalex-snapshot
Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae628openalex-snapshot
OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu309openalex-snapshot
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz538openalex-snapshot
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity
inferred← citeshttps://doi.org/10.1093/nar/gkp368openalex-snapshot
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes
inferred← citeshttps://doi.org/10.1096/fj.12-216119openalex-snapshot
Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein
inferred← citeshttps://doi.org/10.1097/j.pain.0000000000000273openalex-snapshot
COMT gene locus
inferred← citeshttps://doi.org/10.1098/rsif.2011.0584openalex-snapshot
Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches
inferred← citeshttps://doi.org/10.1101/2021.09.13.460049openalex-snapshot
Convex-PL R – Revisiting affinity predictions and virtual screening using physics-informed machine learning
inferred← citeshttps://doi.org/10.1101/2023.09.26.559597openalex-snapshot
Septins Enable T Cell Contact Guidance via Amoeboid-Mesenchymal Switch
inferred← citeshttps://doi.org/10.1101/2025.05.27.656443openalex-snapshot
A Diffusion-Based Framework for Designing Molecules in Flexible Protein Pockets
inferred← citeshttps://doi.org/10.1101/2025.09.30.679569openalex-snapshot
PSP-0119: Targeted IRAK4 Degradation as a Novel Therapeutic Strategy for FLT3-Mutant AML
inferred← citeshttps://doi.org/10.1109/bibm.2016.7822757openalex-snapshot
Geometry based general prediction model of protein-peptide binding affinities
inferred← citeshttps://doi.org/10.1109/smc53992.2023.10393924openalex-snapshot
Scoring Protein-Ligand Complex Structures by HybridNet
inferred← citeshttps://doi.org/10.1109/tcbb.2022.3204188openalex-snapshot
Predicting Drug-Target Interactions Via Dual-Stream Graph Neural Network
inferred← citeshttps://doi.org/10.1111/bph.15463openalex-snapshot
Identification and characterization of novel candidate compounds targeting 6‐ and 7‐transmembrane μ‐opioid receptor isoforms
inferred← citeshttps://doi.org/10.11131/2016/101202openalex-snapshot
Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors
inferred← citeshttps://doi.org/10.1126/sciadv.1700479openalex-snapshot
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations
inferred← citeshttps://doi.org/10.1145/3453483.3454042openalex-snapshot
Fluid: a framework for approximate concurrency via controlled dependency relaxation
inferred← citeshttps://doi.org/10.1158/2326-6066.c.6550485openalex-snapshot
Data from Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling
inferred← citeshttps://doi.org/10.1158/2326-6066.cir-20-0451openalex-snapshot
Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling
inferred← citeshttps://doi.org/10.1186/1744-8069-8-25openalex-snapshot
Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase Activity
inferred← citeshttps://doi.org/10.1186/s13321-023-00795-9openalex-snapshot
Structure-based, deep-learning models for protein-ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1261/rna.075937.120openalex-snapshot
Ensemble switching unveils a kinetic rheostat mechanism of the eukaryotic thiamine pyrophosphate riboswitch
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002499openalex-snapshot
Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005690openalex-snapshot
TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006859openalex-snapshot
Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations
inferred← citeshttps://doi.org/10.1371/journal.pone.0024287openalex-snapshot
Structural Mechanism of S-Adenosyl Methionine Binding to Catechol O-Methyltransferase
inferred← citeshttps://doi.org/10.1371/journal.pone.0142826openalex-snapshot
Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation
inferred← citeshttps://doi.org/10.1515/psr-2020-0034openalex-snapshot
Computational methods for calculation of protein-ligand binding affinities in structure-based drug design
inferred← citeshttps://doi.org/10.1517/17460441.2013.794780openalex-snapshot
Automated docking for novel drug discovery
inferred← citeshttps://doi.org/10.17615/f82n-3148openalex-snapshot
Exploration of the role of CIB1 in cell survival and tumor growth
inferred← citeshttps://doi.org/10.17615/swtm-yd33openalex-snapshot
Developing a Bioscavenger Against Organophosphate Nerve Agents
inferred← citeshttps://doi.org/10.2174/0929867325666180514110824openalex-snapshot
Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.2174/1381612811319120005openalex-snapshot
Scoring Functions for Prediction of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.2174/1568026620666200618123026openalex-snapshot
Identification of Potential Inhibitors for Targets Involved in Dengue Fever
inferred← citeshttps://doi.org/10.2174/1574893614666191003125540openalex-snapshot
Docking Techniques in Toxicology: An Overview
inferred← citeshttps://doi.org/10.26434/chemrxiv.11910870openalex-snapshot
Learning RMSD to Improve Protein-Ligand Scoring and Pose Selection
inferred← citeshttps://doi.org/10.26434/chemrxiv.11910870.v2openalex-snapshot
Learning RMSD to Improve Protein-Ligand Scoring and Pose Selection
inferred← citeshttps://doi.org/10.31031/madd.2018.01.000518openalex-snapshot
Molecular Docking an Important Tool for Drug Designing
inferred← citeshttps://doi.org/10.3389/fmolb.2022.867241openalex-snapshot
NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules
inferred← citeshttps://doi.org/10.3390/cancers16010050openalex-snapshot
Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models
inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/ijms252312676openalex-snapshot
Incorporating Water Molecules into Highly Accurate Binding Affinity Prediction for Proteins and Ligands
inferred← citeshttps://doi.org/10.3390/molecules200713384openalex-snapshot
Molecular Docking and Structure-Based Drug Design Strategies
inferred← citeshttps://doi.org/10.3390/molecules26237369openalex-snapshot
Virtual Screening with Gnina 1.0
inferred← citeshttps://doi.org/10.3390/molecules28031324openalex-snapshot
Computer-Aided Drug Design towards New Psychotropic and Neurological Drugs
inferred← citeshttps://doi.org/10.3390/molecules28041661openalex-snapshot
Machine Learning Scoring Functions for Drug Discovery from Experimental and Computer-Generated Protein–Ligand Structures: Towards Per-Target Scoring Functions
inferred← citeshttps://doi.org/10.3410/f.727797185.793538420openalex-snapshot
Faculty Opinions recommendation of Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch009openalex-snapshot
Scoring Functions of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch030openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch036openalex-snapshot
Scoring Functions of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.4018/979-8-3693-5598-5.ch012openalex-snapshot
Molecular Docking
inferred← citeshttps://doi.org/10.4172/2167-7956.1000166openalex-snapshot
Computational Issues of Protein-Ligand Docking
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/10.5204/thesis.eprints.242134openalex-snapshot
Molecular modelling and machine learning for the investigation of 2-oxazolidinone ribosomal antibacterials
inferred← citeshttps://doi.org/10.6084/m9.figshare.26660296openalex-snapshot
Additional file 1 of Structure-based, deep-learning models for protein-ligand binding affinity prediction
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