ReviewJournal of the Royal Society, Interface2012
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.
Review in Journal of the Royal Society, Interface, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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
39 citing papers in PubMed.
- Design, synthesis, and anticancer evaluation of novel pyrrole-pyrazoline/chalcone hybrids:RSC medicinal chemistry · 2026Article
- Isomer-Dependent Pharmacokinetic Behavior and VKOR Interactions of Second-Generation Anticoagulant Rodenticides: An Integrated In Vivo-In Vitro-In Silico Investigation.International journal of molecular sciences · 2026Article
- Graphene Nanoplatelets Suppress Foam Cell Formation and Atherogenic Inflammation in Macrophages.Cellular and molecular bioengineering · 2026Article
- Comparative inhibitory effects of phillyrin and phillygenin on elastase: mechanisms and therapeutic potential.Frontiers in nutrition · 2026Article
- Skin-Integrated Soft Wearable XR Interfaces for Seamless and Realistic User Experience.Chemical reviews · 2025Review
- In Silico Analysis of CMolecules (Basel, Switzerland) · 2025Article
- AI-driven rational design of promiscuous and selective plastic-binding peptides.Chemical science · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Exploring Marine-Derived Compounds: In Silico Discovery of Selective Ketohexokinase (KHK) Inhibitors for Metabolic Disease Therapy.Marine drugs · 2024Article
- Therapeutic potential ofFrontiers in chemistry · 2024Article
- Synthesis, antimicrobial activity and molecular docking study of benzyl functionalized benzimidazole silver(I) complexes.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2023Article
- Synergistic Inhibitory Effect of Quercetin and Cyanidin-3O-Sophoroside on ABCB1.International journal of molecular sciences · 2023Article
- Surface ID: a geometry-aware system for protein molecular surface comparison.Bioinformatics (Oxford, England) · 2023Article
- Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants.Computational and structural biotechnology journal · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency.Biomolecules · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Binding Site Switch by Dispersion Interactions: Rotational Signatures of Fenchone-Phenol and Fenchone-Benzene Complexes.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- AnalyzingFrontiers in molecular biosciences · 2020Article
- Binding site matching in rational drug design: algorithms and applications.Briefings in bioinformatics · 2019Review
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
No grant is acknowledged in the PubMed record.
Abstract
The recognition process between a protein and a partner represents a significant theoretical challenge. In silico structure-based drug design carried out with nothing more than the three-dimensional structure of the protein has led to the introduction of many compounds into clinical trials and numerous drug approvals. Central to guiding the discovery process is to recognize active among non-active compounds. While large-scale computer simulations of compounds taken from a library (virtual screening) or designed de novo are highly desirable in the post-genomic area, many technical problems remain to be adequately addressed. This article presents an overview and discusses the limits of current computational methods for predicting the correct binding pose and accurate binding affinity. It also presents the performances of the most popular algorithms for exploring binary and multi-body protein interactions.
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.