AlignMe: an update of the web server for alignment of membrane protein sequences

Staritzbichler, René; Yaklich, Emily; Sarti, Edoardo; Ristic, Nikola; Hildebrand, Peter W.; Forrest, Lucy R.

doi:10.1093/nar/gkac391

Cited by 4 publications

(5 citation statements)

References 35 publications

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“…AlignMe is a software package and webserver for detecting similarities between proteins too low to be detected on the sequence level using standard methods ( 24 ). AlignMe is optimized for membrane proteins, but not limited to them.…”

Section: Methods and Descriptionmentioning

confidence: 99%

“…MutationExplorer joins our series of web services available at our platform http://proteinformatics.org which we aspire to support and maintain long-term: ProteinPrompt ( 33 ), MDCiao [Pérez Hernández, G. and Tiwari, S. (March, 2024)], Voronoia ( 34 ), Sierra Platinum Service( 35 ), AlignMe ( 24 ). MutationExplorer is freely available to all users online without any login requirement at: http://proteinformatics.org/mutation_explorer .…”

Section: Data Availabilitymentioning

confidence: 99%

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MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts

Philipp,

Moth,

Ristic

et al. 2024

Nucleic Acids Research

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The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format. Structures are flexibly colorable, not only by energetic differences, but also by hydrophobicity, sequence conservation, or other biochemical profiling. Coloring by interface score reveals mutation impacts on binding surfaces. MutationExplorer strives for efficiency in user experience. For example, we have prepared 45 000 PDB depositions for instant retrieval and initial display. All modeling steps are performed by Rosetta. Visualizations leverage MDsrv/Mol*. MutationExplorer is available at: http://proteinformatics.org/mutation_explorer/.

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Section: Methods and Descriptionmentioning

confidence: 99%

“…MutationExplorer joins our series of web services available at our platform http://proteinformatics.org which we aspire to support and maintain long-term: ProteinPrompt ( 33 ), MDCiao [Pérez Hernández, G. and Tiwari, S. (March, 2024)], Voronoia ( 34 ), Sierra Platinum Service( 35 ), AlignMe ( 24 ). MutationExplorer is freely available to all users online without any login requirement at: http://proteinformatics.org/mutation_explorer .…”

Section: Data Availabilitymentioning

confidence: 99%

MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts

Philipp,

Moth,

Ristic

et al. 2024

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…M utation E xplorer joins our series of web services available at our platform http://proteinformatics.org which we aspire to support and maintain long-term: ProteinPrompt [30], MDCiao [31], Voronoia [32], Sierra Platinum Service[33], alignme [21]. M utation E xplorer is freely available to all users online without any login requirement at: http://proteinformatics.org/mutation_explorer The MDSRV implementation on which M utation E xplorer is build is available at: http://proteinformatics.org/mdsrv-web The interface for alignment servers is available at: https://github.com/starbeachlab/explorer_interface Issues with the website can be reported at: https://github.com/starbeachlab/MutationExplorerServer/issues…”

Section: Availabilitymentioning

confidence: 99%

“…AlignMe ALIGNME is a software package and webserver for detecting similarities between proteins too low to be detected on the sequence level using standard methods [21]. ALIGNME is optimized for membrane proteins, but not limited to them.…”

Section: Webservermentioning

confidence: 99%

“…MUTATIONEXPLORER joins our series of web services available at our platform http://proteinformatics.org which we aspire to support and maintain long-term: ProteinPrompt [30], MDCiao [31], Voronoia [32], Sierra Platinum Service [33], AlignMe [21]. MUTATIONEXPLORER is freely available to all users online without any login requirement at: http://proteinformatics.org/mutation_explorer…”

Section: Availabilitymentioning

confidence: 99%

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MutationExplorer- a webserver for mutation of proteins and 3D visualization of energetic impacts

Philipp

Moth

Ristic

et al. 2023

Preprint

Self Cite

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The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MUTATIONEXPLORER webserver maps variants onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MUTATIONEXPLORER can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Structures are flexibly colorable, not only by energetic differences, but also by hydrophobicity, or sequence conservation, or other biochemical profiling. Another mutation source can be human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format. MUTATIONEXPLORER strives for efficiency in user experience. For example, we have prepared 45,000 PDB depositions for instant retrieval and initial display. All modeling steps are performed by Rosetta. Visualizations leverage MDsrv/Mol*. MUTATIONEXPLORER is available at: http://proteinformatics.org/mutation_explorer/

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Template-based modeling of insect odorant receptors outperforms AlphaFold3 for ligand binding predictions

Jabeen,

Oakeshott,

Lee

et al. 2024

Sci Rep

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Insects rely on odorant receptors (ORs) to detect and respond to volatile environmental cues, so the ORs are attracting increasing interest as potential targets for pest control. However, experimental analysis of their structures and functions faces significant challenges. Computational methods such as template-based modeling (TBM) and AlphaFold3 (AF3) could facilitate the structural characterisation of ORs. This study first showed that both models accurately predicted the structural fold of MhOR5 , a jumping bristletail OR with known experimental 3D structures, although accuracy was higher in the extracellular region of the protein and binding mode of their cognate ligands with TBM. The two approaches were then compared for their ability to predict the empirical binding evidence available for OR-odorant complexes in two economically important fruit fly species, Bactrocera dorsalis and B. minax . Post-simulation analyses including binding affinities, complex and ligand stability and receptor-ligand interactions (RLIs) revealed that TBM performed better than AF3 in discriminating between binder and non-binder complexes. TBM’s superior performance is attributed to hydrophobicity-based helix-wise multiple sequence alignment (MSA) between available insect OR templates and the ORs for which the binding data were generated. This MSA identified conserved residues and motifs which could be used as anchor points for refining the alignments. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-024-80094-x.

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AlignMe: an update of the web server for alignment of membrane protein sequences

Cited by 4 publications

References 35 publications

MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts

MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts

MutationExplorer- a webserver for mutation of proteins and 3D visualization of energetic impacts

Template-based modeling of insect odorant receptors outperforms AlphaFold3 for ligand binding predictions

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