ArticleJournal of computational chemistry2017
Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Linker Engineering of Hybrid Triazole-Thiazolidine Antifungals Identifies a Promising Lead Against Drug-ResistantPharmaceuticals (Basel, Switzerland) · 2026Article
- DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.Journal of computer-aided molecular design · 2026Article
- TaLiRAGen: target-aware ligand generation via retrieval-augmented large language models.Molecular diversity · 2026Article
- Expanding the Palette of Molecular Fragments for Small Molecule De Novo Design Through Isosteric Swapping.Journal of computational chemistry · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Salidroside protects against myocardial infarction via activating MIF-mediated mitochondrial quality control.Chinese medicine · 2025Article
- Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK.Journal of computational chemistry · 2025Article
- Azole Homodimers as Promising Antifungal Agents: Synthesis, Biological Activity Evaluation and Molecular Modeling.Current medicinal chemistry · 2025Article
- Synthesis and Biological Evaluation of a Series of New Hybrid Amide Derivatives of Triazole and Thiazolidine-2,4-dione.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening.Journal of chemical information and modeling · 2024Article
- Recent Advances in Automated Structure-Based De Novo Drug Design.Journal of chemical information and modeling · 2024Review
- Geometric Deep Learning for Structure-Based Ligand Design.ACS central science · 2023Article
- Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit.Journal of chemical information and modeling · 2023Article
- Article
- Role of the voltage‑gated sodium channel Nav1.6 in glioma and candidate drugs screening.International journal of molecular medicine · 2023Article
- Review
- A molecular evolution algorithm for ligand design in DOCK.Journal of computational chemistry · 2022Article
- FastGrow: on-the-fly growing and its application to DYRK1A.Journal of computer-aided molecular design · 2022Article
- LIMO: Latent Inceptionism for Targeted Molecule Generation.Proceedings of machine learning research · 2022Article
- DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design.Molecules (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
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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.