ArticleNucleic acids research2010
Multi-Harmony: detecting functional specificity from sequence alignment.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed, 74 citations in OpenAlex.
- PCA-Based Database Mining Enables the Discovery of Bacterial Carbene Transferases for Stereodivergent Cyclopropanation.Angewandte Chemie (International ed. in English) · 2026Article
- Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses.Journal of molecular evolution · 2025Article
- Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals.eLife · 2024Article
- Slc11 Synapomorphy: A Conserved 3D Framework Articulating Carrier Conformation Switch.International journal of molecular sciences · 2023Article
- Principal Component and Structural Element Analysis Provide Insights into the Evolutionary Divergence of Conotoxins.Biology · 2022Article
- The biological feasibility and social context of gene-edited, caffeine-free coffee.Food science and biotechnology · 2022Review
- Nramp: Deprive and conquer?Frontiers in cell and developmental biology · 2022Article
- Recognition of fold- and function-specific sites in the ligand-binding domain of the thyroid hormone receptor-like family.Frontiers in endocrinology · 2022Article
- Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication.G3 (Bethesda, Md.) · 2021Article
- Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings.Protein science : a publication of the Protein Society · 2021Article
- Expanded roles for the MutL family of DNA mismatch repair proteins.Yeast (Chichester, England) · 2021Review
- Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications.Frontiers in bioengineering and biotechnology · 2021Article
- Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl.Frontiers in molecular biosciences · 2021Article
- Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter.Nature communications · 2020Article
- Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies.Nucleic acids research · 2020Article
- DIP/Dpr interactions and the evolutionary design of specificity in protein families.Nature communications · 2020Article
- Article
- HLA Class I Downregulation by HIV-1 Variants from Subtype C Transmission Pairs.Journal of virology · 2018Article
- Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.BMC evolutionary biology · 2017Article
- Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases.The Journal of biological chemistry · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein-protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww.
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.