ReviewMethods (San Diego, Calif.)2017
In silico structure-based approaches to discover protein-protein interaction-targeting drugs.
Review in Methods (San Diego, Calif.), 2017. 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
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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
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.
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Who cites it
39 citing papers in PubMed, 87 citations in OpenAlex.
- Pep2Mol: 3D Molecule Generation Targeting Protein-Protein Interfaces with Diffusion Models.bioRxiv : the preprint server for biology · 2026Article
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- Docking of millions: accelerating a million-scale virtual screening using deep learning.Briefings in bioinformatics · 2026Article
- Drug Delivery System for the Anticancer Drug Paclitaxel Using Lipocalin-Type Prostaglandin D Synthase Conjugated to a Tumor-Targeting Peptide.ACS omega · 2026Article
- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
- Alphappimi: a comprehensive deep learning framework for predicting PPI-modulator interactions.Journal of cheminformatics · 2025Article
- Insights into Binding Mechanisms of Potential Inhibitors Targeting PCSK9 Protein via Molecular Dynamics Simulation and Free Energy Calculation.Molecules (Basel, Switzerland) · 2025Article
- In Silico Identification of Potential Antagonists Targeting the HPV16 E2-E1 Interaction: A Step Toward Novel Therapeutics for Cervical Cancer.Current issues in molecular biology · 2025Article
- Interface-aware molecular generative framework for protein-protein interaction modulators.Journal of cheminformatics · 2024Article
- New insights into protein-protein interaction modulators in drug discovery and therapeutic advance.Signal transduction and targeted therapy · 2024Review
- Article
- Recent Deep Learning Applications to Structure-Based Drug Design.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties.Molecules (Basel, Switzerland) · 2023Article
- Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: Pharmacophore-based virtual screening, molecular docking, molecular dynamics and binding free energy studies.Journal of molecular liquids · 2023Article
- Artificial Intelligence and Machine Learning Technology Driven Modern Drug Discovery and Development.International journal of molecular sciences · 2023Review
- Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions.Frontiers in oncology · 2023Review
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- Solubility-Aware Protein Binding Peptide Design Using AlphaFold.Biomedicines · 2022Article
- Machine Learning in Drug Discovery: A Review.Artificial intelligence review · 2022Article
- DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions.Frontiers in chemistry · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A core concept behind modern drug discovery is finding a small molecule that modulates a function of a target protein. This concept has been successfully applied since the mid-1970s. However, the efficiency of drug discovery is decreasing because the druggable target space in the human proteome is limited. Recently, protein-protein interaction (PPI) has been identified asan emerging target space for drug discovery. PPI plays a pivotal role in biological pathways including diseases. Current human interactome research suggests that the number of PPIs is between 130,000 and 650,000, and only a small number of them have been targeted as drug targets. For traditional drug targets, in silico structure-based methods have been successful in many cases. However, their performance suffers on PPI interfaces because PPI interfaces are different in five major aspects: From a geometric standpoint, they have relatively large interface regions, flat geometry, and the interface surface shape tends to fluctuate upon binding. Also, their interactions are dominated by hydrophobic atoms, which is different from traditional binding-pocket-targeted drugs. Finally, PPI targets usually lack natural molecules that bind to the target PPI interface. Here, we first summarize characteristics of PPI interfaces and their known binders. Then, we will review existing in silico structure-based approaches for discovering small molecules that bind to PPI interfaces.
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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.