ArticleJournal of computational chemistry2016
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- In silico discovery of umami peptides: From sequence-based intelligent models to structure-function mechanistic insight.Current research in food science · 2026Review
- Exploring the Potential Mechanisms of Danshen for the Treatment of Ulcerative Colitis based on Serum Pharmacochemistry, Gene Expression Profiling, and Network Pharmacology: Regulation of Cell Apoptosis and Inflammatory Response.Current computer-aided drug design · 2026Article
- Exploiting the Achilles' heel of cancer through a structure-based drug-repurposing approach and experimental validation of top drugs using the TRAP assay.Molecular diversity · 2025Article
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
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- Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking.Journal of chemical information and modeling · 2025Article
- CHARMM-GUIJournal of chemical theory and computation · 2025Article
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- Evaluating the Mechanism Underlying Multi-Compound Synergy of Banxia Decoction in the Treatment of Hashimoto's Thyroiditis Based on Network Pharmacology and Molecular Docking.International journal of general medicine · 2025Article
- Triterpene esters from Uncaria rhynchophylla hooks as potent HIV-1 protease inhibitors and their molecular docking study.Scientific reports · 2024Article
- Novel hybrids of 1,2,3-triazole-benzoxazole: design, synthesis, and assessment of DprE1 enzyme inhibitors using fluorometric assay and computational analysis.Journal of enzyme inhibition and medicinal chemistry · 2024Article
- Ancestral Sequence Reconstruction to Enable Biocatalytic Synthesis of Azaphilones.Journal of the American Chemical Society · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- A Computational Approach to Understanding and Predicting the Edulcorant Profile of Glucosyl Steviol Glycosides.Foods (Basel, Switzerland) · 2024Article
- Mechanistic docking in terpene synthases using EnzyDock.Methods in enzymology · 2024Review
- Identification of Novel Protein Targets of Prodigiosin for Breast Cancer Using Inverse Virtual Screening Methods.Applied biochemistry and biotechnology · 2023Article
- In Silico Studies of Novel Vemurafenib Derivatives as BRAF Kinase Inhibitors.Molecules (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.