Predicting target DNA sequences of DNA-binding proteins based on unbound structures. [PDF]
PLoS ONE, 2012 DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions.
Chien-Yu Chen +5 more
doaj +1 more source
Base-sequence-dependent sliding of proteins on DNA [PDF]
Physical Review E, 2004 The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general
Barbi, Maria +3 more
openaire +6 more sources
Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2. [PDF]
PLoS ONE, 2011 BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors.
Nina Winter +4 more
doaj +1 more source
A linear model for transcription factor binding affinity prediction in protein binding microarrays. [PDF]
PLoS ONE, 2011 Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a protein's affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity ...
Matti Annala +3 more
doaj +1 more source
A Novel Image Cryptosystem Inspired by the Generation of Biological Protein Sequences
IEEE Access, 2023 Image encryption is essential to keep images secure either in personal devices or over the cloud drives. Various robust image cryptosystems have been implemented during the past decades to keep the encrypted images far from illegal decryption by ...
Mohammad Nassef +2 more
doaj +1 more source
Back-translation for discovering distant protein homologies [PDF]
, 2009 Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin.
A. Pedersen +17 more
core +10 more sources
DNA Motif Recognition Modeling from Protein Sequences
iScience, 2018 Summary: Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still ...
Ka-Chun Wong
doaj +1 more source
Outline of a genome navigation system based on the properties of GA-sequences and their flanks. [PDF]
PLoS ONE, 2009 Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments.
Guenter Albrecht-Buehler
doaj +1 more source
Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA) [PDF]
, 2013 The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage
A Ghosh +48 more
core +10 more sources
Investigations into the molecular effects of single nucleotide polymorphism [PDF]
, 2000 Objectives: DNA sequences are very rich in short repeats and their pattern can be altered by point mutations. We wanted to investigate the effect of single nucleotide polymorphism (SNP) on the pattern of short DNA repeats and its biological consequences.
Lohrer, Horst D., Tangen, Uwe
core +1 more source