ReviewStructure (London, England : 1993)2013
Protein modeling: what happened to the "protein structure gap"?
Review in Structure (London, England : 1993), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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
52 citing papers in PubMed, 130 citations in OpenAlex.
- Carba-NAD binding activates SIR2 by reshaping conformational plasticity and rewiring long-range allosteric networks.PLoS computational biology · 2026Article
- Genome-wide identification and characterization of DUF789 genes in cotton: implications for fibre development.BMC plant biology · 2025Article
- High-speed atomic force microscopy and 3D modeling reveal the structural dynamics of ADAR1 complexes.Nature communications · 2025Article
- AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.Protein science : a publication of the Protein Society · 2025Article
- SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer.Computational and structural biotechnology journal · 2024Article
- Reducing Immunogenicity by Design: Approaches to Minimize Immunogenicity of Monoclonal Antibodies.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2024Review
- Analysis of nonsynonymous SNPs in candidate genes that influence bovine temperament and evaluation of their effect in Brahman cattle.Molecular biology reports · 2024Article
- A primer to directed evolution: current methodologies and future directions.RSC chemical biology · 2023Review
- Beyond sequence: Structure-based machine learning.Computational and structural biotechnology journal · 2023Review
- 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.GigaScience · 2022Article
- Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal.Biology · 2022Article
- Structure and dynamics of membrane protein in SARS-CoV-2.Journal of biomolecular structure & dynamics · 2022Article
- AlphaFold2 models indicate that protein sequence determines both structure and dynamics.Scientific reports · 2022Article
- Molecular insights into the interaction of HPV-16 E6 variants against MAGI-1 PDZ1 domain.Scientific reports · 2022Article
- Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks.NAR genomics and bioinformatics · 2021Article
- High-yield production of L-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum.Microbial cell factories · 2020Article
- QMEANDisCo-distance constraints applied on model quality estimation.Bioinformatics (Oxford, England) · 2020Article
- Engineering cytochrome P450 enzyme systems for biomedical and biotechnological applications.The Journal of biological chemistry · 2020Review
- Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal · 2020Review
- Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling.PLoS computational biology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Computational modeling of three-dimensional macromolecular structures and complexes from their sequence has been a long-standing vision in structural biology. Over the last 2 decades, a paradigm shift has occurred: starting from a large "structure knowledge gap" between the huge number of protein sequences and small number of known structures, today, some form of structural information, either experimental or template-based models, is available for the majority of amino acids encoded by common model organism genomes. With the scientific focus of interest moving toward larger macromolecular complexes and dynamic networks of interactions, the integration of computational modeling methods with low-resolution experimental techniques allows the study of large and complex molecular machines. One of the open challenges for computational modeling and prediction techniques is to convey the underlying assumptions, as well as the expected accuracy and structural variability of a specific model, which is crucial to understanding its limitations.
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.