#NARWebServicesIssue
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bffo.bsky.social
In the @narjournal.bsky.social #NARWebServicesIssue | RNA motifs, RNA structure, and motif context analyzed by RNAanalyzer | #Bioinformatics #Webserver #OpenScience #Genomics #RNA | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
RNA motifs, RNA structure, and motif context analyzed by RNAanalyzer3
Abstract. RNAanalyzer3 (“RNA analyzer cubic”; https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de) substitutes the frequently consulted current RNAanal
academic.oup.com
May 4, 2026 at 1:03 PM
bffo.bsky.social
In @narjournal.bsky.social #NARWebServicesIssue | ChIP-Atlas 2025 update: 10-year anniversary of a data-mining platform for exploring #epigenomic landscape | #Bioinformatics #Webserver #OpenScience #Genomics #ChIP | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
ChIP-Atlas 2025 update: 10-year anniversary of a data-mining platform for exploring epigenomic landscape
Abstract. ChIP-Atlas (https://chip-atlas.org/) is a data-mining platform that systematically processes and integrates public epigenomic profiling data, inc
academic.oup.com
April 30, 2026 at 1:19 PM
bffo.bsky.social
From @jmbujnicki.bsky.social and colleagues in the @narjournal.bsky.social #NARWebServicesIssue | #ARTEM server: an online tool for nucleic acid #3DMotif searches, #3DStructure superposition and structure-based #Alignment | #Webserver #Bioinformatics | 🧬🖥️🧪🔓🇵🇱
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academic.oup.com/nar/advance-...
ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment
Abstract. ARTEM Server is an online platform for comparative analysis of nucleic acid 3D structures, combining two complementary superposition methods base
academic.oup.com
May 6, 2026 at 12:29 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARWebServicesIssue | BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline | #Bioinformatics #WebServer #OpenScience #Proteomics #AphaFold | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline
Abstract. BilboMD is a web-accessible platform that facilitates integrative modeling of flexible macromolecules using experimental small-angle X-ray and ne
academic.oup.com
April 28, 2026 at 12:08 PM
bffo.bsky.social
In the @narjournal.bsky.social #NARWebServicesIssue | Comparative structural analysis of #protein complexes with SPICE | #Bioinformatics #Webserver #OpenScience #Proteomics #DataViz #PDB #PPI | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
Comparative structural analysis of protein complexes with SPICE
Abstract. Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein–protein interac
academic.oup.com
May 5, 2026 at 12:13 PM
bffo.bsky.social
From @ramonduran.bsky.social and colleagues in @narjournal.bsky.social #NARWebServicesIssue | FoldDelay web server: an online tool to quantify #translation -driven delays in #protein native contact formation | #Bioinformatics #Webserver #OpenScience | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
FoldDelay web server: an online tool to quantify translation-driven delays in protein native contact formation
Abstract. Co-translational protein folding is shaped by the vectorial nature of translation, which causes residues to emerge sequentially from the ribosome
academic.oup.com
April 29, 2026 at 3:00 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARWebServicesIssue | ShapeRNA: an integrated web server for #RNA #Secondary #Structure, ensemble, and functional analysis | #Bioinformatics #WebServices #OpenScience #RNASecondaryStructure | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis
Abstract. RNA secondary structure plays a critical role in gene regulation, yet existing computational and experimental tools for structure analysis are of
academic.oup.com
April 24, 2026 at 4:34 PM
bffo.bsky.social
In @narjournal.bsky.social #NARWebServicesIssue | xBind: an integrated #webserver for large language model-enabled cross-molecular protein binding site prediction | #Bioinformatics #OpenScience #PPI #ProteinDNABinding #ProteinRNABinding #AlphaFold #LLM | 🧬 🖥️ 🧪🔓
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academic.oup.com/nar/advance-...
xBind: an integrated webserver for large language model-enabled cross-molecular protein binding site prediction
Abstract. xBind is an interactive, freely accessible, and fully configurable webserver for large language model (LLM)-enabled cross-molecular protein bindi
academic.oup.com
May 6, 2026 at 12:15 PM
bffo.bsky.social
In @narjournal.bsky.social #NARWebServicesIssue | #PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles | #Bioinformatics #Webserver #OpenScience #Proteomics #Druggability | 🧬🖥️🧪🔓 🇫🇷
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academic.oup.com/nar/advance-...
PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles
Abstract. PockFlex is a web server designed to analyse pockets across protein structural ensembles and support the reconstruction, characterisation, and pr
academic.oup.com
May 9, 2026 at 12:21 PM
bffo.bsky.social
In the @narjournal.bsky.social #NARWebServicesIssue | #DAVID: a #WebServer for #functional #annotation and functional #enrichment #analysis of #GeneLists (2025 update) | #Bioinformatics #OpenScience #Education | 🧬🖥️🧪🔓
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academic.oup.com/nar/advance-...
DAVID: a web server for functional annotation and functional enrichment analysis of gene lists (2025 update)
Abstract. DAVID is a widely used bioinformatics resource that provides functional annotation and functional enrichment analysis for gene and protein lists
academic.oup.com
May 9, 2026 at 12:05 PM
bffo.bsky.social
In the @narjournal.bsky.social #NARWebServicesIssue | CB-Dock3: an enhanced web server for protein-ligand blind docking | #Bioinformatics #WebServer #OpenScience #Protein #Ligand #Binding #BlindDocking | 🧬🖥️🧪🔓
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academic.oup.com/nar/advance-...
CB-Dock3: an enhanced web server for protein–ligand blind docking
Abstract. Elucidating protein–ligand interactions is pivotal for understanding biological mechanisms and accelerating drug discovery. Blind docking, which
academic.oup.com
May 7, 2026 at 12:26 PM
bffo.bsky.social
In the @narjournal.bsky.social #NARWebServicesIssue | AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts | #Bioinformatics #WebServer #OpenScience #Database #Proteomics #AlphaFold | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts
Abstract. The availability of large-scale protein structure collections enables structure-based analysis of their function and evolution beyond what is pos
academic.oup.com
April 25, 2026 at 4:15 PM
bffo.bsky.social
From @cryptogenomicon.bsky.social and colleagues in the @narjournal.bsky.social #NARWebServicesIssue | #HMMER web server: 2026 update | #Bioinformatics #WebServer #OpenScience #Proteomics | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
HMMER web server: 2026 update
Abstract. The HMMER web server, available at https://www.ebi.ac.uk/Tools/hmmer, provides online access to tools from the HMMER software suite (http://hmmer
academic.oup.com
April 28, 2026 at 12:19 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARWebServicesIssue | PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in #metagenomic data | #Bioinformatics #WebServices #OpenScience #Metagenome #Virus | 🧬 🖥️ 🧪 🔓
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academic.oup.com/nar/advance-...
PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data
Abstract. Metagenomic sequencing has transformed virus discovery; however, downstream bioinformatic analyses for viral identification, classification, and
academic.oup.com
April 24, 2026 at 3:29 PM
bffo.bsky.social
From @doelsnitz.bsky.social & colleagues in the @narjournal.bsky.social #NARWebServicesIssue | Ligify 2.0: a web server for predicted #SmallMolecule #Biosensors | #Bioinformatics #WebServer #OpenScience #Prokaryotic #TranscriptionFactors #TFs | 🧬🖥️🧪🔓
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academic.oup.com/nar/advance-...
Ligify 2.0: a web server for predicted small molecule biosensors
Abstract. Prokaryotic transcription factors (TFs) serve as small molecule biosensors with broad applications in biotechnology, yet only a fraction have bee
academic.oup.com
May 7, 2026 at 12:21 PM
bffo.bsky.social
In @narjournal.bsky.social #NARWebServicesIssue | T2T-Hub: a central platform for analyzing #Plant and #Animal telomere-to-telomere genomes | #Bioinformatics #Webserver #OpenScience #Genomics #WGS #T2T | 🧬🖥️🧪🔓
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academic.oup.com/nar/advance-...
T2T-Hub: a central platform for analyzing plant and animal telomere-to-telomere genomes
Abstract. T2T-Hub is a free, web-based platform designed to facilitate the analysis and visualization of telomere-to-telomere (T2T) genomes in plants and a
academic.oup.com
May 7, 2026 at 12:08 PM