• iDNA-Prot

  • Referenced in 16 articles [sw22410]
  • iDNA-Prot: identification of DNA binding proteins using random forest with grey model. DNA-binding ... tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges ... Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based ... tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server...
  • PseDNA-Pro

  • Referenced in 6 articles [sw22424]
  • PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation ... Identification of DNA-binding proteins is an important problem in biomedical research as DNA-binding ... into Support Vector Machine (SVM) for DNA-binding protein identification. The proposed method is called ... combination of various features for DNA-binding protein prediction is a suitable approach...
  • DPP-PseAAC

  • Referenced in 5 articles [sw24764]
  • PseAAC: a DNA-binding protein prediction model using Chou’s general pseaac. A DNA-binding ... protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification ... predicting whether a protein can bind with a DNA or not. In this paper ... proposed method, named as {it DNA-binding Protein Prediction model using Chou’s general PseAAC...
  • ChIPmix

  • Referenced in 4 articles [sw35320]
  • high-throughput technology to investigate DNAprotein binding or chromatin/histone modifications. ChIP–chip data require...
  • NUCPLOT

  • Referenced in 4 articles [sw16870]
  • Protein-Nucleic Acid Interactions. Proteins that bind to DNA are found in all areas ... which residues are involved in binding to the DNA and how they interact with ... covalent bonds between the protein and the DNA. The resulting diagram is both clear ... which can be used for any protein-DNA complex and will also work for certain...
  • nDNA-prot

  • Referenced in 1 article [sw34402]
  • nDNA-prot: identification of DNA-binding proteins based on unbalanced classification. Results: In this paper ... than the traditional methods in identifying DNA-binding proteins. The identification was conducted using ... method can help to accurately identify DNA-binding proteins, and the web server is accessible ... addition, we also predicted possible DNA-binding protein sequences in all of the sequences from...
  • TRANSFAC

  • Referenced in 73 articles [sw17201]
  • factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ). Its content ... scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about...
  • UniPROBE

  • Referenced in 3 articles [sw18504]
  • online database of protein-binding microarray data on proteinDNA interactions. The Universal PBM Resource ... repository of information on the DNA-binding preferences of proteins as determined by universal protein...
  • Starr

  • Referenced in 2 articles [sw20401]
  • ChIP-chip) is an assay for DNA-protein-binding or post-translational chromatin/histone modifications ... related proteins, or of binding profiles of the same protein in different genetic backgrounds ... mechanistic understanding of the effects of DNA binding events on gene expression. We present...
  • Apbsmem

  • Referenced in 4 articles [sw22298]
  • increase the binding of one protein to another and facilitate protein-DNA and protein-ligand...
  • MEME

  • Referenced in 14 articles [sw15711]
  • MEME: discovering and analyzing DNA and protein sequence motifs. MEME (Multiple EM for Motif Elicitation ... discovery of new transcription factor binding sites and protein domains. MEME works by searching ... ungapped sequence patterns that occur in the DNA or protein sequences provided by the user...
  • pyDNase

  • Referenced in 1 article [sw17300]
  • enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges ... involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied ... many years been used to identify specific binding sites occupied by TFs at individual ... data surrounding proteinDNA interactions that allows accurate prediction of occupied TF binding sites...
  • ChIP-PaM

  • Referenced in 1 article [sw22385]
  • ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data. BACKGROUND: ChIP ... binding sites. However, high cost and high rate of false discovery of transcription factor binding ... algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines...
  • MotifDb

  • Referenced in 1 article [sw20751]
  • MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs. More than 2000 annotated position...
  • StackDPPred

  • Referenced in 0 articles [sw34125]
  • StackDPPred: a stacking based prediction of DNA-binding protein from sequence. Motivation: Identification ... DNA-binding proteins from only sequence information is one of the most challenging problems ... field of genome annotation. DNA-binding proteins play an important role in various biological processes ... splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus...
  • WoLF PSORT

  • Referenced in 11 articles [sw27721]
  • protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features ... composition and functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest ... ways: (i) a list of proteins of known localization with the most similar localization features...
  • COMODE

  • Referenced in 3 articles [sw36145]
  • DNA binding sites using the information derived from structural characteristics of protein-DNA interactions ... data. Some of the transcription factor binding data of Lee et al. (2002) were also...
  • COMPASS

  • Referenced in 9 articles [sw23109]
  • method allows prediction of relationships between protein families in the PFAM database beyond the range ... intricate homology between the DNA-binding domain of the CTF/NFI family and the MH1 domain...
  • GeneReporter

  • Referenced in 2 articles [sw24071]
  • protein families, domains, potential cofactors, structure, function, cellular localization, metabolic contribution and corresponding DNA binding...
  • Nebula

  • Referenced in 1 article [sw16944]
  • binding sites of transcription factors and other DNA-associated proteins. We present a web service...