ArticleProteins2012
BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed.
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Protein-Ligand Blind Docking Using CB-Dock2.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Synthesis of Pyrrolo[3,4-Pharmaceuticals (Basel, Switzerland) · 2023Article
- Machine learning assessment of the binding region as a tool for more efficient computational receptor-ligand docking.Journal of molecular liquids · 2022Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- Residue-Residue Interaction Prediction via Stacked Meta-Learning.International journal of molecular sciences · 2021Article
- FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening.Journal of chemical information and modeling · 2021Article
- Immunoediting role for major vault protein in apoptotic signaling induced by bacterialProceedings of the National Academy of Sciences of the United States of America · 2021Article
- A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa.Structure (London, England : 1993) · 2021Article
- Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.Molecules (Basel, Switzerland) · 2021Article
- Big data and artificial intelligence discover novel drugs targeting proteins without 3D structure and overcome the undruggable targets.Stroke and vascular neurology · 2020Review
- Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand-Receptor Interactions.Journal of molecular biology · 2020Article
- EDock: blind protein-ligand docking by replica-exchange monte carlo simulation.Journal of cheminformatics · 2020Article
- Maturation Mechanism of Nitrile Hydratase FromFrontiers in microbiology · 2020Article
- CB-Dock: a web server for cavity detection-guided protein-ligand blind docking.Acta pharmacologica Sinica · 2020Article
- Stalis: A Computational Method for Template-Based Ab Initio Ligand Design.Journal of computational chemistry · 2019Article
- Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints.Journal of computer-aided molecular design · 2019Article
- Interaction of rs316019 variants of SLC22A2 with metformin and other drugs- anJournal, genetic engineering & biotechnology · 2018Article
- FINDSITEJournal of chemical information and modeling · 2018Article
- Genome-Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco.International journal of molecular sciences · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We developed BSP-SLIM, a new method for ligand-protein blind docking using low-resolution protein structures. For a given sequence, protein structures are first predicted by I-TASSER; putative ligand binding sites are transferred from holo-template structures which are analogous to the I-TASSER models; ligand-protein docking conformations are then constructed by shape and chemical match of ligand with the negative image of binding pockets. BSP-SLIM was tested on 71 ligand-protein complexes from the Astex diverse set where the protein structures were predicted by I-TASSER with an average RMSD 2.92 Å on the binding residues. Using I-TASSER models, the median ligand RMSD of BSP-SLIM docking is 3.99 Å which is 5.94 Å lower than that by AutoDock; the median binding-site error by BSP-SLIM is 1.77 Å which is 6.23 Å lower than that by AutoDock and 3.43 Å lower than that by LIGSITE(CSC) . Compared to the models using crystal protein structures, the median ligand RMSD by BSP-SLIM using I-TASSER models increases by 0.87 Å, while that by AutoDock increases by 8.41 Å; the median binding-site error by BSP-SLIM increase by 0.69Å while that by AutoDock and LIGSITE(CSC) increases by 7.31 Å and 1.41 Å, respectively. As case studies, BSP-SLIM was used in virtual screening for six target proteins, which prioritized actives of 25% and 50% in the top 9.2% and 17% of the library on average, respectively. These results demonstrate the usefulness of the template-based coarse-grained algorithms in the low-resolution ligand-protein docking and drug-screening. An on-line BSP-SLIM server is freely available at http://zhanglab.ccmb.med.umich.edu/BSP-SLIM.
Indexed as
Identifiers
What OpenQuestion holds
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.