ReviewCurrent opinion in structural biology2015
Template-based prediction of protein function.
Review in Current opinion in structural biology, 2015. 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.
- Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces.Journal of chemical information and modeling · 2025Article
- ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Review
- HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry.Journal of molecular biology · 2020Article
- MADOKA: an ultra-fast approach for large-scale protein structure similarity searching.BMC bioinformatics · 2019Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network.PLoS computational biology · 2019Article
- Functional classification of protein structures by local structure matching in graph representation.Protein science : a publication of the Protein Society · 2018Article
- LIBRA-WA: a web application for ligand binding site detection and protein function recognition.Bioinformatics (Oxford, England) · 2018Article
- Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level.Global heart · 2017Review
- Modeling complexes of modeled proteins.Proteins · 2017Article
- A hybrid method for protein-protein interface prediction.Protein science : a publication of the Protein Society · 2016Article
- Unexpected features of the dark proteome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.International journal of molecular sciences · 2015Review
- Modeling enzyme-ligand binding in drug discovery.Journal of cheminformatics · 2015Review
- Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis.Journal of cellular physiology · 2015Article
- Functional prediction of hypothetical proteins in human adenoviruses.Bioinformation · 2015Article
- Integrating 3D structural information into systems biology.The Journal of biological chemistryReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
We discuss recent approaches for structure-based protein function annotation. We focus on template-based methods where the function of a query protein is deduced from that of a template for which both the structure and function are known. We describe the different ways of identifying a template. These are typically based on sequence analysis but new methods based on purely structural similarity are also being developed that allow function annotation based on structural relationships that cannot be recognized by sequence. The growing number of available structures of known function, improved homology modeling techniques and new developments in the use of structure allow template-based methods to be applied on a proteome-wide scale and in many different biological contexts. This progress significantly expands the range of applicability of structural information in function annotation to a level that previously was only achievable by sequence comparison.
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.