Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods modeling the sequence specificity of binding. However, none studies has utilized graph convolutional for motif inference. In this work, we propose to use We build a k-mer whole dataset based on co-occurrence relationship then learn DNA Graph ...

Significance In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve individual diffusional steps on DNA. Here, we report mainly all-atom equilibrium simulations a WRKY domain in association with and We demonstrate complete stepping cycle one base pair within microseconds, stochastic mo...

the binding of drugs by plasma proteins is an important phenomenon, because it influences the size of the free fraction of the drugs in plasma. in this study the influence of dipyridamole (dp) on the protein binding of propranolol (pl) and pl on the protein binding of dp were studied alone and in the presence of nicotine (nc).        the equilibrium dialysis was employed for protein binding stu...

background and objective: neisseria meningitidis is a leading cause of meningitis and sepsis worldwide. the factor h binding protein (fhbp) is a key virulence factor of neisseria meningitidis that is able to selectively bind to human factor h, the key regulator of the alternative complement pathway, which it has important implications for meningococcal pathogene- sis and vaccine design. the aim...

A subset of DNA replication proteins of herpes simplex virus (HSV) comprising the single-strand DNA-binding protein, ICP8 (UL29), and the helicase-primase complex (UL5, UL8, and UL52 proteins) has previously been shown to be sufficient for the replication of adeno-associated virus (AAV). We recently demonstrated complex formation between ICP8, AAV Rep78, and the single-stranded DNA AAV genome, ...

Abstract The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome systems, the most common which type I Par system. It consists adapter protein, ParB, that binds to DNA cargo via interaction with parS sequence; and ATPase, ParA, nonspecific mediates transport. However, molecular details how this s...

background: acanthamoeba keratitis develops by pathogenic acanthamoeba such as a. pal­es­tinen­sis . indeed this species is one of the known causative agents of amoebic keratitis in iran. mannose binding protein (mbp) is the main pathogenicity factors for developing this sight threatening disease. we aimed to characterize mbp gene in pathogenic acanthamoeba isolates such as a. palestinensis . m...

Protein and DNA have vital role in our biological processes. For accurately predicting binding protein, develop a new sequence based prediction method from the protein sequence. Sequence only considers information as input. DBP, first reliable benchmark data set bank. Second, using Amino Acid Composition (AAC), Position Specific Scoring Matrix (PSSM), Predicted Solvent Accessibility (PSA), Prob...