ArticleBMC structural biology2013
DINC: a new AutoDock-based protocol for docking large ligands.
Article in BMC structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Evaluation of Human-Approved Active Pharmaceutical Ingredients Against Lactate Dehydrogenase from Theileria annulata.Acta parasitologica · 2026Article
- DINC-ensemble: A web server for docking large ligands incrementally to an ensemble of receptor conformations.Journal of molecular biology · 2025Article
- Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50.Protein science : a publication of the Protein Society · 2025Article
- Immunoinformatics-Based Design of Multi-epitope DNA and mRNA Vaccines Against Zika Virus.Bioinformatics and biology insights · 2024Article
- Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management.Scientific reports · 2023Review
- Synthesis, In Silico Studies, and In Vitro Anti-Inflammatory Activity of Novel Imidazole Derivatives Targeting p38 MAP Kinase.ACS omega · 2023Article
- Drug and Anti-Viral Peptide Design to Inhibit the Monkeypox Virus by Restricting A36R Protein.Bioinformatics and biology insights · 2022Article
- Structural Prediction of Peptide-MHC Binding Modes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe.Briefings in bioinformatics · 2021Article
- Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach.Biophysical chemistry · 2021Article
- Accelerating AutoDock4 with GPUs and Gradient-Based Local Search.Journal of chemical theory and computation · 2021Article
- HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.JCO clinical cancer informatics · 2020Article
- In silico vaccine design againstNetwork modeling and analysis in health informatics and bioinformatics · 2020Article
- Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.BMC molecular and cell biology · 2019Article
- General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept.Scientific reports · 2018Article
- Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.Current topics in medicinal chemistry · 2018Review
- Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration.Scientific reports · 2017Article
- DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.Cancer research · 2017Article
- Targeting the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 6 (STAT6) with Cell-Permeable, Phosphatase-Stable Phosphopeptide Mimics Potently Inhibits Tyr641 Phosphorylation and Transcriptional Activity.Journal of medicinal chemistry · 2015Article
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3 authors.
Funding
Abstract
backgroundUsing the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow.
resultsIn our earlier work, we presented a novel AutoDock-based incremental protocol (DINC) that addresses the limitations of AutoDock's standard protocol by enabling improved docking of large ligands. Instead of docking a large ligand to a target protein in one single step as done in the standard protocol, our protocol docks the large ligand in increments. In this paper, we present three detailed examples of docking using DINC and compare the docking results with those obtained using AutoDock's standard protocol. We summarize the docking results from an extended docking study that was done on 73 protein-ligand complexes comprised of large ligands. We demonstrate not only that DINC is up to 2 orders of magnitude faster than AutoDock's standard protocol, but that it also achieves the speed-up without sacrificing docking accuracy. We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand. Finally, we introduce a webserver for docking large ligands using DINC.
conclusionsDocking large ligands using DINC is significantly faster than AutoDock's standard protocol without any loss of accuracy. Therefore, DINC could be used as an alternative protocol for docking large ligands. DINC has been implemented as a webserver and is available at http://dinc.kavrakilab.org. Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands could benefit from DINC and its webserver implementation.
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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.