ArticleBMC bioinformatics2009
VASCo: computation and visualization of annotated protein surface contacts.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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
44 citing papers in PubMed.
- Dynamics driving the precursor in NifEN scaffold during nitrogenase FeMo-cofactor assembly.Nature chemical biology · 2026Article
- The ATP-independent dihydro-2-phenanthroyl-CoA reductase AprC catalyzes two consecutive two-electron reduction steps of dihydro-2-phenanthroyl-CoA to hexahydro-2-phenanthroyl-CoA in anaerobic phenanthrene degradation.Applied and environmental microbiology · 2026Article
- Sad from Proteobacteria is a Structurally Distinct ALDH3 Enzyme Specialized for the Oxidation of Steroidal Aldehydes.Biochemistry · 2025Article
- Re-engineering a transferase scaffold for indole C3 methylation in diketopiperazines.Protein science : a publication of the Protein Society · 2025Article
- AMPEC4:Molecules (Basel, Switzerland) · 2025Article
- Selected Polyphenols of Polish Poplar Propolis as a Key Component Shaping Its Antibacterial Properties-In Vitro and In Silico Approaches.Molecules (Basel, Switzerland) · 2025Article
- Article
- Efficacy of EGFR tyrosine kinase inhibitors in patients with non-small cell lung cancer with EGFR exon 19 insertions: clinical-genomic, preclinical analysis through LC-SCRUM-Asia (multi-institutional genomic screening registry).Lung cancer (Amsterdam, Netherlands) · 2025Article
- Human Embryonic Kidney HEK293 Cells as a Model to Study SMVT-Independent Transport of Biotin and Biotin-Furnished Nanoparticles in Targeted Therapy.International journal of molecular sciences · 2025Article
- Biochemical and structural elucidation of the L-carnitine degradation pathway of the human pathogenFrontiers in microbiology · 2024Article
- Comparative in silico analysis of CNS-active molecules targeting the blood-brain barrier choline transporter for Alzheimer's disease therapy.In silico pharmacology · 2024Article
- Article
- Residue-Specific Incorporation of the Non-Canonical Amino Acid Norleucine Improves Lipase Activity on Synthetic Polyesters.Frontiers in bioengineering and biotechnology · 2022Article
- Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates.Nature communications · 2020Article
- PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids.Journal of molecular modeling · 2020Article
- FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates.Molecular cell · 2019Article
- Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase.Chembiochem : a European journal of chemical biology · 2019Article
- Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.Scientific reports · 2017Article
- Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein-Protein Interactions.Molecules (Basel, Switzerland) · 2017Article
- Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies.Cell reports · 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStructural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions.
resultsVASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in.
conclusionVASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.
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.