ArticleComputational and structural biotechnology journal2024
Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.
Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Article
- Structural Diversity and Differential Natural Pairings of MAT1-1-1 and MAT1-2-1 Proteins Essential for Sexual Reproduction inInternational journal of molecular sciences · 2026Article
- AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level.Protein science : a publication of the Protein Society · 2026Article
- Transferrin receptor 1-mediated iron uptake supports thermogenic activation in human cervical-derived adipocytes.FEBS letters · 2026Article
- Multiple disulfide-bonded states confer extensive conformational diversity in fibrinogen.Protein science : a publication of the Protein Society · 2026Article
- Molecular Modeling of the Pathogenetic Mechanisms of Neuropsychiatric Disorders.International journal of molecular sciences · 2026Review
- Fast prediction of protein flexibility.Bioinformatics (Oxford, England) · 2026Article
- Article
- Using AlphaFold3 for the Interrogation of Protein Disulfide Bonds.Methods in molecular biology (Clifton, N.J.) · 2026Article
- From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.Advances in experimental medicine and biology · 2026Review
- AI-driven insights into protein misfolding and innate immunity in neurodegenerative diseases.Frontiers in immunology · 2026Review
- Article
- CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.Nucleic acids research · 2025Article
- Selective Modulation of PAR-2-Driven Inflammatory Pathways by Oleocanthal: Attenuation of TNF-α and Calcium Dysregulation in Colorectal Cancer Models.International journal of molecular sciences · 2025Article
- Virtual Screening and Molecular Dynamics of Cytokine-Drug Complexes for Atherosclerosis Therapy.International journal of molecular sciences · 2025Article
- Three-Dimensional Structural Heteromorphs of Mating-Type Proteins inJournal of fungi (Basel, Switzerland) · 2025Article
- AlphaFold in protein structure and function prediction.Computational and structural biotechnology journal · 2025Article
- EquilibraTor streamlines molecular dynamics simulations in a single execution.Computational and structural biotechnology journal · 2025Article
- MSF-CPMP: A novel multi-source feature fusion model for prediction of cyclic peptide membrane permeability.Computational and structural biotechnology journal · 2025Article
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
CABS-flex is a well-established method for fast protein flexibility simulations, offering an effective balance between computational efficiency and accuracy in modeling protein dynamics. To further enhance its predictive capabilities, we propose incorporating AlphaFold's predicted Local Distance Difference Test (pLDDT) scores into CABS-flex simulations. The pLDDT scores, which reflect the confidence of AlphaFold's structural predictions, were integrated with secondary structure information to refine the restraint schemes used in the simulations. We tested this approach on the ATLAS database, which includes molecular dynamics (MD) simulations of nearly 1400 proteins. The results showed improved alignment of flexibility predictions with the MD data compared to previous restraint schemes. The integration of pLDDT scores also offers a new perspective on protein flexibility by incorporating structural confidence into the analysis. This development enhances the utility of CABS-flex for investigating protein dynamics and motion.
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.