ArticleBMC bioinformatics2013
Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 312 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
312 citing papers in PubMed, 569 citations in OpenAlex.
- Design and in silico evaluation of PV-GNProtecta: an mRNA multi-epitope vaccine candidate against Puumala virus using immunoinformatics and structural analysis.Genomics & informatics · 2026Article
- Generation and MHC class II loading of an endogenous influenza epitope revealed by a T cell receptor-like antibody.bioRxiv : the preprint server for biology · 2026Article
- Subtractive Proteomics and Immunoinformatics-Guided Design of a Multi-Epitope Vaccine Against Aspergillus fumigatus.Probiotics and antimicrobial proteins · 2026Article
- Aglycosylated Immunoglobulin G1 Fc Stabilized Through Disulfide Bond Addition Exhibits Compositional Homogeneity and Retains Fc γ Receptor IIIa/CD16a Binding.Antibodies (Basel, Switzerland) · 2026Article
- Designing potent and immunogenic epitope based peptide vaccine against all serotypes of DENV via structural, physico-chemical and immunoinformatics-based approaches.Scientific reports · 2026Article
- Immunoinformatics-based design of artificial chimeric proteins as universal vaccine candidates against foot-and-mouth disease virus serotypes A, O, and SAT2.Scientific reports · 2026Article
- Computational design and molecular characterization of a multi-epitope peptide vaccine targeting pancreatic cancer.Journal, genetic engineering & biotechnology · 2026Article
- In Silico Design and Computational Characterization of Novel Chimeric Multiepitope Antigens for Mpox Serosurveillance: An Immunoinformatics Approach.Health science reports · 2026Article
- A conserved capsid-based multi-epitope vaccine targeting dengue virus serotypes (DENV1-4): an integrated computational and in vivo study.BMC immunology · 2026Article
- An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase.bioRxiv : the preprint server for biology · 2026Article
- Characterisation of a cold-adapted, thermostable glucokinase from psychrophilic Pseudoalteromonas sp. AS-131 reveals how the enzyme achieves high thermal stability without loss of cold adaptation.The FEBS journal · 2026Article
- From Sequence to Solution: Computational Design of a Multi-Epitope Vaccine Candidate Against Francisella tularensis.Probiotics and antimicrobial proteins · 2026Article
- A bioinformatics pipeline for the design of a SART3-targeted cancer vaccine with enhanced immunogenicity.Genomics & informatics · 2026Article
- Molecular characterization and immunoinformatics-based design of a multi-epitope vaccine against Staphylococcus nepalensis.Antonie van Leeuwenhoek · 2026Article
- Multi-tope subunit vaccine for human anthrax through pan-genome-based reverse vaccinology approach.Molecular genetics and genomics : MGG · 2026Article
- Identification and evaluation of tumor pyroptosis-associated antigens for design a vaccine candidate against lung cancer.Scientific reports · 2026Article
- Design of a global population-covering multi-epitope mRNA vaccine against Lassa virus using immunoinformatics.Scientific reports · 2026Article
- In Silico Design and Characterization of a Multi-Epitope Vaccine Candidate AgainstMicroorganisms · 2026Article
- Computational design of a novel multi-epitope vaccine candidate against group A rotavirus.Virology journal · 2026Article
- Functional characterization of a dockerin-containing expansin-like protein from the anaerobic fungus Neocallimastix californiae.Biotechnology for biofuels and bioproducts · 2026Article
252 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDisulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines.
resultsWe had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number of limitations including a Windows platform dependency. Here, we introduce Disulfide by Design 2.0 (DbD2), a web-based, platform-independent application that significantly extends functionality, visualization, and analysis capabilities beyond the original program. Among the enhancements to the software is the ability to analyze the B-factor of protein regions involved in predicted disulfide bonds. Importantly, this feature facilitates the identification of potential disulfides that are not only likely to form but are also expected to provide improved thermal stability to the protein.
conclusionsDbD2 provides platform-independent access and significantly extends the original functionality of DbD. A web server hosting DbD2 is provided at http://cptweb.cpt.wayne.edu/DbD2/.
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.