The Phyre2 web portal for protein modelling, prediction and analysis
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Summary
An updated protocol for Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants for a user's protein sequence.
- Type
- article
- Published
- 2015-05-07
- Cited by
- 9,118
- References
- 37
- Access
- Open access
- OpenAlex
- https://openalex.org/W1803102843
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:17312187
Keywords
Computational biology, Computer science, Bioinformatics, Biology
References
- ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web
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- Predicting functionally important residues from sequence conservation
- The structure of the protein universe and genome evolution
- Protein Folding Requires Crowd Control in a Simulated Cell
- Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
- Template-based protein structure modeling using the RaptorX web server
- Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.
- SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features
- Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
- I-TASSER: a unified platform for automated protein structure and function prediction
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- A method and server for predicting damaging missense mutations
- Protein structure prediction on the Web: a case study using the Phyre server
- fpocket: online tools for protein ensemble pocket detection and tracking
- Cyclic coordinate descent: A robotics algorithm for protein loop closure
- 3DLigandSite: predicting ligand-binding sites using similar structures
- Improving the accuracy of transmembrane protein topology prediction using evolutionary information
- CDD: conserved domains and protein three-dimensional structure
- Critical assessment of methods of protein structure prediction (CASP) — round x
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- Crystal structures of APOBEC3G N-domain alone and its complex with DNA
- Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis
- Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706)
- PRIMO: An Interactive Homology Modeling Pipeline
- Heterogeneous antigenic properties of the porcine reproductive and respiratory syndrome virus nucleocapsid
- Multifunctional Thioredoxin-Like Protein from the Gastrointestinal Parasitic Nematodes Strongyloides ratti and Trichuris suis Affects Mucosal Homeostasis
- TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol
- Ligand-Biased Regulation of PtdIns(3,4,5)P3-Dependent Signal Transduction in GPCR Control of Pituitary Hormone Release
- An Insight into the Secondary Metabolism of Muscodor yucatanensis: Small-Molecule Epigenetic Modifiers Induce Expression of Secondary Metabolism-Related Genes and Production of New Metabolites in the Endophyte
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- Insights into the Structure, Function, and Ion-Mediated Signaling Pathways Transduced by Plant Integrin-Linked Kinases
- Herbicide targets and detoxification proteins in sugarcane: from gene assembly to structure modelling.
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- Biochemical characterization and comparison of aspartylglucosaminidases secreted in venom of the parasitoid wasps Asobara tabida and Leptopilina heterotoma
- A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti
- ROS induced distribution of mitochondria to filopodia by Myo19 depends on a class specific tryptophan in the motor domain
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