ArticleJournal of computational chemistry2015
DOCK 6: Impact of new features and current docking performance.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 360 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
360 citing papers in PubMed.
- AI-driven discovery of natural product-derived FAK1 inhibitors for idiopathic pulmonary fibrosis.Molecular diversity · 2026Article
- Large-scale comparative virtual screening identifies novel molecular targets underlying the multi-target activity of quercetin in psoriasis.Inflammopharmacology · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Big Data and Artificial Intelligence in Cancer Drug Discovery: Promise, Challenges, and Emerging Opportunities.Cancers · 2026Review
- From Detoxified Yam to Bioactive Extracts: Integrated Extraction and In Silico Evidence of Anti-Biofilm Activity ofLife (Basel, Switzerland) · 2026Article
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- Precomputed grid potential (PGP) method: Exact reciprocal-space acceleration of particle mesh Ewald for Monte Carlo simulations.The Journal of chemical physics · 2026Article
- Computational investigation for exploring botanical ingredients as potential negative allosteric modulators targeting metabotropic glutamate receptor 5.Research in pharmaceutical sciences · 2026Article
- Can Cavity Prediction Algorithms Help in Docking Experiments?Journal of computational chemistry · 2026Article
- Combining Artificial Intelligence and Human Expertise in Pursuit of Novel PolQ Inhibitors.ACS omega · 2026Article
- Two faces of drug repurposing data in machine learning-driven structure-based virtual screening supported by interaction fingerprints.Journal of computer-aided molecular design · 2026Article
- DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.Journal of computer-aided molecular design · 2026Article
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 2026Article
- DockingDB: An online reverse-docking database for plant hormone research.Plant communications · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Molecular and Analytical Understanding of Resveratrol Interactions for Advanced Biotechnological Applications.Molecules (Basel, Switzerland) · 2026Review
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- Integrative In Silico and In Vivo Evidence of Quercetin as a Multitarget Neuroprotective Agent in Alzheimer's Disease.ACS omega · 2026Article
- COFFEE-PRESC: A Fast Prescreening Method Using Compound Retrieval by Pairwise Positional Relationship of Representative Fragments.Journal of chemical information and modeling · 2026Article
- CHARMM-GUIJournal of chemical information and modeling · 2026Article
300 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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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.