MimoDB 2.0: a mimotope database and beyond

Huang, Jian; Ru, Beibei; Zhu, Ping; Nie, Fulei; Yang, Jun; Wang, Xuyang; Dai, Peng; Lin, Hao; Guo, Feng‐Biao; Rao, Nini

doi:10.1093/nar/gkr922

Cited by 109 publications

(94 citation statements)

References 36 publications

(34 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It has enabled the discovery of ligands for hundreds of targets, yet the literature still contains several poorly-explained observations: (1) identical sequences could emerge from unrelated screens for unrelated target [22,23], and (2) screens that should yield a large number of diverse ligand often yield only one sequence motif (reviewed in [16]). The nearly complete sequence coverage of libraries illuminates the origin of these observations.…”

Section: Introductionmentioning

confidence: 99%

“…Choice of the library: In this report, we sequence a commercially-available library of random 12mers from New England Biolabs (Ph.D-12). This library has been used in ~800 publications (source of estimate: PLoMics database http://www.treeofmedicine.com/phagedisplay and MimoDB database [22,23]). According to the manufacturer (NEB), naïve library contains up to 10 9 different sequences.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Deep sequencing analysis of phage libraries using Illumina platform

Matochko

Chu

Jin

et al. 2012

Methods

105

111

View full text Add to dashboard Cite

This paper presents an analysis of phage-displayed libraries of peptides using Illumina. We describe steps for the preparation of the short DNA fragments for deep sequencing and MatLab software for the analysis of the results. Screening of peptide libraries displayed on the surface of bacteriophage (phage display) can be used to discover peptides that bind to any target. The key step in this discovery is the analysis of peptide sequences present in the library. This analysis is usually performed by Sanger sequencing, which is labor intensive and limited to examination of a few hundred phage clones. On the other hand, Illumina deep-sequencing technology can characterize over 10 7 reads in a single run. We applied Illumina sequencing to analyze phage libraries. Using PCR, we isolated variable regions from a M13KE phage vector. The PCR primers contained (i) sequences flanking the variable region, (ii) barcodes, and (iii) variable 5'-terminal region. We used this approach to examine how diversity of peptides in phage display libraries changes as a result of amplification of libraries in bacteria. Using HiSeq single-end Illumina sequencing of these fragments, we acquired over 2x10 7 reads, 57 base pairs (bp) in length. Each read contained information about the barcode (6 bp), one complimentary region (12 bp) and a variable region (36 bp). We applied this sequencing to a model library of 10 6 unique clones and observed that amplification enriches ~150 clones, which dominate ~20% of the library. Deep sequencing, for the first time, characterized the collapse of diversity in phage libraries. The results suggest that screens based on repeated amplification and small-scale sequencing identify a few binding clones and miss thousands of useful clones. The deep sequencing approach described here could identify under-represented clones in phage screens. It could also be instrumental in developing new screening strategies, which can preserve diversity of phage clones and identify ligands previously lost in phage display screens.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Deep sequencing analysis of phage libraries using Illumina platform

Matochko

Chu

Jin

et al. 2012

Methods

105

111

View full text Add to dashboard Cite

show abstract

“…All these methods have succeeded in some case studies. These test cases were either compiled from published papers or from special databases such as the ASPD database (Valuev, et al, 2002) and the MimoDB database (Huang, et al, 2012;Ru, et al, 2010). However, no systematic evaluations were done when these methods were published.…”

Section: Benchmarking Tools Of the Tradementioning

confidence: 99%

“…As the protein structure and mimotope data increase rapidly (Huang, et al, 2012;Rose, et al, 2011), now it becomes possible to make benchmarks for the trade to evaluate its tools at a larger scale. Sun et al compiled a benchmark from the PDB database and the MimoDB database.…”

Section: Benchmarking Tools Of the Tradementioning

confidence: 99%

See 1 more Smart Citation

Prediction of Protein Interaction Sites Using Mimotope Analysis

Huang¹,

Ru²,

Dai³

2012

Protein-Protein Interactions - Computational and Experimental Tools

View full text Add to dashboard Cite

Expression AnalysisIn Vitro

Colosimo

2013

Encyclopedia of Life Sciences

View full text Add to dashboard Cite

Expression analysis in vitro is a constantly evolving field, consolidated in the fourth quarter of the last century and essentially based on the use of a template of ribonucleic acid (RNA) , for a translation reaction, or of deoxyribonucleic acid (DNA) , in a coupled transcription–translation system. Traditional applications of expression analysis in vitro cover a wide range of structural and functional studies on proteins and nucleotides using methodologies like yeast one‐, two‐ and three‐hybrid systems, reporter genes, phage display, DNase footprinting, methylation interference assays and gel‐shift assays. Moreover, in the last decades in‐vitro expression analyses benefitted from substantial advancements, mostly associated with the use of a number of refined cell‐free protein synthesis methods and of microarrays and nanodevices. The frequency trends of related keywords in a huge database of English books published all over the world and covering a wide, recent time window provide an indirect – although highly suggestive – estimate of their relative importance in the next years. Key Concepts: In‐vitro expression systems can: (1) be used for the expression of toxic, proteolytically sensitive or unstable proteins; (2) incorporate unnatural amino acids and (3) allow the addition of exogenous factors to study enzymatic activity, and of microsomal membranes to study post‐translational modifications. Application of in‐vitro expression systems include: (1) site‐specific methods that utilise tRNA charged with any number of unnatural amino acids; (2) the use of putative DNA‐binding proteins such as transcription factors and (3) improving particular features of preexisting molecules like ultraspecificity, affinity and reaction rate. The intrinsic appealing of in‐vitro expression analysis has been reinforced in the last decades thanks to refined cell‐free protein synthesis (CFPS) methods, microarrays (MA) and nanodevices (ND), whose evolution occurred at a remarkably fast pace. The data flow streaming out of the above‐mentioned techniques demands, in any case, massive statistical analyses and systematic cross‐checking of results by independent strategies.

show abstract

MimoDB 2.0: a mimotope database and beyond

Cited by 109 publications

References 36 publications

Deep sequencing analysis of phage libraries using Illumina platform

Deep sequencing analysis of phage libraries using Illumina platform

Prediction of Protein Interaction Sites Using Mimotope Analysis

Expression AnalysisIn Vitro

Contact Info

Product

Resources

About