3D-Footprint

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3D-Footprint

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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3d-footprint

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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Other names: 3d-footprint

Estimates of DNA-binding specificity for protein-DNA complexes in PDB

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Publications

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3D-footprint: a database for the structural analysis of protein-DNA complexes
PMID: 19767616

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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http://nar.oxfordjournals.org/content/38/suppl_1/D91

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• 3D-footprint: a database for the structural analysis of protein-DNA complexes PubMed citations: 32.

  32 articles citing: 3D-footprint: a database for the structural analysis of protein-DNA complexes

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  SBSA: an online service for somatic binding sequence annotation. PMID:34606615

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  On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF. PMID:33575598

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  RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. PMID:31871587

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  DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments. PMID:31793988

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  DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957

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  SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. PMID:31477007

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  On a Robust, Sensitive Cell-Free Method for Pseudomonas Sensing and Quantification in Microfluidic Templated Hydrogels. PMID:31370199

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  A strong NF-κB p65 responsive cis-regulatory sequence from Arabidopsis thaliana interacts with WRKY40. PMID:31197450

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  DNA-protein interaction: identification, prediction and data analysis. PMID:30915687

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  Transcription factors involved in basal immunity in mammals and plants interact with the same MAMP-responsive cis-sequence from Arabidopsis thaliana. PMID:30467788

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  DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. PMID:28431131

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  Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PMID:27690309

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  Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis. PMID:27384774

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  An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237

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  Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast. PMID:26484765

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  A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. PMID:26130577

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  An overview of the prediction of protein DNA-binding sites. PMID:25756377

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  DBBP: database of binding pairs in protein-nucleic acid interactions. PMID:25474259

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  Structure-based modeling of protein: DNA specificity. PMID:25414269

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  Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. PMID:24773781

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  OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors. PMID:23703395

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  PiDNA: Predicting protein-DNA interactions with structural models. PMID:23703214

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  Analyzing and building nucleic acid structures with 3DNA. PMID:23644419

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  The twilight zone of cis element alignments. PMID:23268451

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  NPIDB: Nucleic acid-Protein Interaction DataBase. PMID:23193292

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  TFinDit: transcription factor-DNA interaction data depository. PMID:22943312

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  Atomistic modeling of protein-DNA interaction specificity: progress and applications. PMID:22796087

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  3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. PMID:22693215

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  SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. PMID:22573174

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  Benchmarks for flexible and rigid transcription factor-DNA docking. PMID:22044637

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  The Protein-DNA Interface database. PMID:20482798

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  Protein databases on the internet. PMID:18265344
• http://nar.oxfordjournals.org/content/38/suppl_1/D91

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nucleotide sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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transcriptional regulator sites and transcription factors

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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proteins

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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protein binding sites

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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structure analysis

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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sequence composition, complexity and repeats

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.375340

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nucleic acid sequence transcription proteins protein binding sites structure analysis sequence composition, complexity and repeats