ReviewQuarterly reviews of biophysics2012
Protein flexibility in docking and surface mapping.
Review in Quarterly reviews of biophysics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed.
- Stable simulations do not guarantee functional engagement: a case study of off-target prediction for Seladelpar and Zanamivir.Journal of computer-aided molecular design · 2026Article
- Integrating modern computational techniques elevates binding mode identification for molecular fragments.Molecular diversity · 2026Article
- In Silico Drug Repositioning Identifies SYK Kinase Inhibitors as Potential Neuroprotective Agents for Ataxia-Telangiectasia.Chemical biology & drug design · 2026Article
- A Reproducible Hierarchical Virtual Screening Framework Integrating Scaffold-Aware Machine Learning, Ensemble Docking, and Molecular Dynamics: Application to IDO1.Journal of chemical information and modeling · 2026Article
- Organosulfur scaffolds as quorum sensing and biofilm modulators in Gram-negative bacteria.FEMS microbiology reviews · 2026Review
- Immunoinformatics-driven multi-epitope vaccine design targeting PSMA, STEAP1, and B7H3 for prostate cancer.Frontiers in medicine · 2026Article
- Antibacterial Drug Discovery: Deep Learning Successes and Challenges through the Structural Biology Lens.Computational and structural biotechnology journal · 2026Review
- 1-Azinyl-1'-Alkenylferrocenes with Anticholinesterase, Antioxidant, and Antiaggregating Activities as Multifunctional Agents for Potential Treatment of Alzheimer's Disease.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Ultra-large library screening with an evolutionary algorithm in Rosetta (REvoLd).Communications chemistry · 2025Article
- From AI-AssistedPharmaceuticals (Basel, Switzerland) · 2025Review
- Decoding the limits of deep learning in molecular docking for drug discovery.Chemical science · 2025Article
- Chemical and Genetic Validation of an Essential Calcium Entry Channel ofACS infectious diseases · 2025Article
- Computable properties of selected monomeric acylphloroglucinols with anticancer and/or antimalarial activities and first-approximation docking study.Journal of molecular modeling · 2025Article
- Silico study: Hepatoprotective effects of capsaicin on the liver of aflatoxin B1-intoxicated mice (Open veterinary journal · 2025Article
- Advancing Amyloid Aggregation Research: A Focus on Innovative Therapies, Molecular Modeling and Nano-Delivery Systems in Alzheimer's Disease.Current drug targets · 2025Review
- Protein language models are performant in structure-free virtual screening.Briefings in bioinformatics · 2024Article
- Cross-Species Molecular Docking Method to Support Predictions of Species Susceptibility to Chemical Effects.Computational toxicology (Amsterdam, Netherlands) · 2024Article
- Identification of potential marine bioactive compounds from brown seaweeds towards BACE1 inhibitors: molecular docking and molecular dynamics simulations approach.In silico pharmacology · 2024Article
- Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking.Frontiers in molecular biosciences · 2024Article
- Artificial Intelligence in Pharmaceutical Technology and Drug Delivery Design.Pharmaceutics · 2023Review
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
Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%. This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.
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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.