ArticleBioinformatics (Oxford, England)2023
Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Coronavirus NSP14 drives internal m7G modification to rewire host splicing and promote viral replication.Nucleic acids research · 2026Article
- A common network of residue-residue contacts underlies interactions between peptides and HLA class II complex.PloS one · 2026Article
- Cardiotrophin-like cytokine factor 1 forms a complex with IL12/IL23p40.Scientific reports · 2025Article
- Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design.ACS omega · 2025Article
- Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction.Virus evolution · 2025Article
- NRGSuite-Qt: a PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions, and the detection of binding-site similarities.Bioinformatics advances · 2025Article
- TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication.Nature communications · 2024Article
- TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication.bioRxiv : the preprint server for biology · 2024Article
- Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication.PLoS biology · 2024Article
- ProCogGraph: a graph-based mapping of cognate ligand domain interactions.Bioinformatics advances · 2024Article
- Ebola Virus VP35 Interacts Non-Covalently with Ubiquitin Chains to Promote Viral Replication Creating New Therapeutic Opportunities.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryComputational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here, we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics. AVAILABILITY AND IMPLEMENTATION: All scripts are available at https://github.com/NRGLab/Surfaces. Surface's documentation is available at https://surfaces-tutorial.readthedocs.io/en/latest/index.html.
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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.