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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0

https://doi.org/10.1021/ci6002637
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Chemoenzymatic synthesis of macrocycles via dynamic kinetic resolution of secondary alcohols
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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
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Binding Free Energy Calculation and Scoring in Small-Molecule Docking
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A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors
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Water molecules at protein–drug interfaces: computational prediction and analysis methods
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Synthesis and initial pharmacology of dual-targeting ligands for putative complexes of integrin αVβ3 and PAR2
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Computational and biophysical methods for the discovery and optimization of covalent drugs
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Incorporation of histone deacetylase inhibition into the structure of a nuclear receptor agonist
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BetaDock: Shape-Priority Docking Method Based on Beta-Complex
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Relative assessment of different statistical instruments and measures for the prediction of promising outcomes using docking, virtual screening and ADMET analysis against HIV-RT
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The latest automated docking technologies for novel drug discovery
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Water in drug design: pitfalls and good practices
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HCovDock: an efficient docking method for modeling covalent protein–ligand interactions
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The covalent docking software landscape: features and applications in drug design
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Building a virtual ligand screening pipeline using free software: a survey
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Development and application of site mapping methods for the design of glycosaminoglycans
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The herbicide acetochlor causes lipid peroxidation by inhibition of glutathione peroxidase activity
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The herbicide acetochlor causes lipid peroxidation by inhibition of glutathione peroxidase 4
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Drug discovery for breast cancer based on big data analytics techniques
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Drug discovery for breast cancer based on big data analytics techniques
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Protein-Ligand Docking Based on ß-shape
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Toward a Robust Search Method for the Protein-Drug Docking Problem
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Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering
inferred← citeshttps://doi.org/10.1124/mol.108.054254openalex-snapshot
Functional Characterization and In Silico Docking of Full and Partial GluK2 Kainate Receptor Agonists
inferred← citeshttps://doi.org/10.1126/science.aaz7381openalex-snapshot
Biocatalytic synthesis of planar chiral macrocycles
inferred← citeshttps://doi.org/10.1142/9789814287197_0009openalex-snapshot
Incorporating Protein Flexibility in Molecular Docking by Molecular Dynamics: Applications to Protein Kinase and Phosphatase Systems
inferred← citeshttps://doi.org/10.1142/s2737599424500038openalex-snapshot
PPARG modulation by bioactive compounds from Salvia officinalis and Glycyrrhiza glabra in type 2 diabetes management: A in silico study
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s17-s7openalex-snapshot
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
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Agonistic effect of polyunsaturated fatty acids (PUFAs) and its metabolites on brain-derived neurotrophic factor (BDNF) through molecular docking simulation
inferred← citeshttps://doi.org/10.1186/s12982-024-00229-3openalex-snapshot
A review of the current trends in computational approaches in drug design and metabolism
inferred← citeshttps://doi.org/10.1186/s43094-025-00862-yopenalex-snapshot
Assessing molecular docking tools: understanding drug discovery and design
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AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
inferred← citeshttps://doi.org/10.1371/journal.pone.0018845openalex-snapshot
Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening
inferred← citeshttps://doi.org/10.1371/journal.pone.0085678openalex-snapshot
istar: A Web Platform for Large-Scale Protein-Ligand Docking
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A computer-based approach for developing linamarase inhibitory agents
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Accounting for water molecules in drug design
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Understanding the challenges of protein flexibility in drug design
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What has virtual screening ever done for drug discovery?
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Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review
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Molecular Recognition and Drug-Lead Identification: What Can Molecular Simulations Tell Us?
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Virtual Screening Strategies in Drug Discovery: A Critical Review
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In Silico Prediction of Cytochrome P450-Mediated Drug Metabolism
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From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspase Inhibitors
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Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective
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Emerging Need of Today: Significant Utilization of Various Databases and Softwares in Drug Design and Development
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Accounting for Induced-Fit Effects in Docking: What is Possible and What is Not?
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Docking Paradigm in Drug Design
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Modeling Reality for Optimal Docking of Small Molecules to Biological Targets
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Receptor Flexibility in Ligand Docking and Virtual Screening
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The First CACHE Challenge – Identifying Binders of the WD-Repeat Domain of Leucine-Rich Repeat Kinase 2
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The First CACHE Challenge – Identifying Binders of the WD-Repeat Domain of Leucine-Rich Repeat Kinase 2
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-ncqsj-v3openalex-snapshot
The First CACHE Challenge – Testing Diverse Virtual Screening Scoring Methods to Identify Potential LRRK2 Binders
inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-rw78sopenalex-snapshot
The Third CACHE Challenge – Finding Ligands Targeting the Macrodomain of SARS-CoV-2 NSP3 Using AI-inspired and Knowledge-Based Approaches.
inferred← citeshttps://doi.org/10.26434/chemrxiv.14568921openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities.
inferred← citeshttps://doi.org/10.26434/chemrxiv.14568921.v1openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities.
inferred← citeshttps://doi.org/10.26434/chemrxiv.9771014openalex-snapshot
Synthesis and Initial Pharmacology of Heterobivalent Ligands Targeting Putative Complexes of Integrin αVβ3 and PAR2
inferred← citeshttps://doi.org/10.26434/chemrxiv.9771014.v1openalex-snapshot
Synthesis and Initial Pharmacology of Heterobivalent Ligands Targeting Putative Complexes of Integrin αVβ3 and PAR2
inferred← citeshttps://doi.org/10.26481/dis.20141008jdopenalex-snapshot
Application of in-silico approaches to cardiovascular disease
inferred← citeshttps://doi.org/10.32469/10355/90175openalex-snapshot
Theoretical and computational modeling of rna-ligand interactions
inferred← citeshttps://doi.org/10.32657/10220/47354openalex-snapshot
Accurately accelerating drug design workflow
inferred← citeshttps://doi.org/10.32657/10356/69603openalex-snapshot
Exploiting receptor flexibility to improve the accuracy of structure-based virtual screening
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Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities.
inferred← citeshttps://doi.org/10.3389/fchem.2020.00343openalex-snapshot
Structure-Based Virtual Screening: From Classical to Artificial Intelligence
inferred← citeshttps://doi.org/10.3389/fphys.2023.1180896openalex-snapshot
Elucidation of the binding mode of organic polysulfides on the human TRPA1 receptor
inferred← citeshttps://doi.org/10.3390/antibiotics12030463openalex-snapshot
Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents
inferred← citeshttps://doi.org/10.3390/biophysica3040044openalex-snapshot
Screening and Analysis of Potential Inhibitors of SHMT2
inferred← citeshttps://doi.org/10.3390/ijerph16060923openalex-snapshot
A Molecular Docking Approach to Evaluate the Pharmacological Properties of Natural and Synthetic Treatment Candidates for Use against Hypertension
inferred← citeshttps://doi.org/10.3390/ijms241411784openalex-snapshot
The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering
inferred← citeshttps://doi.org/10.3390/molecules20058997openalex-snapshot
S4MPLE—Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking
inferred← citeshttps://doi.org/10.3390/ph14100988openalex-snapshot
Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1
inferred← citeshttps://doi.org/10.3390/ph17111540openalex-snapshot
In Silico Study of the Potential Inhibitory Effects on Escherichia coli DNA Gyrase of Some Hypothetical Fluoroquinolone–Tetracycline Hybrids
inferred← citeshttps://doi.org/10.3390/ph17121593openalex-snapshot
In Silico Evaluation of Some Computer-Designed Fluoroquinolone–Glutamic Acid Hybrids as Potential Topoisomerase II Inhibitors with Anti-Cancer Effect
inferred← citeshttps://doi.org/10.3390/ph19091404openalex-snapshot
Sesquiterpene Lactone Derivatives of Ambrosia artemisiifolia Act as Agonists of the Transient Receptor Potential Ankyrin 1 Ion Channel
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A Review on Computational Software Tools for Drug Design and Discovery
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Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.