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Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

https://doi.org/10.1093/nar/gkg922
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Computers and the Theory of Statistics: Thinking the Unthinkable

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score
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Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
inferred← citeshttps://doi.org/10.1101/2023.05.30.542787openalex-snapshot
ULDNA: Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for Protein-DNA Binding Site Prediction
inferred← citeshttps://doi.org/10.1101/514471openalex-snapshot
Ion counting demonstrates a high electrostatic potential of the nucleosome
inferred← citeshttps://doi.org/10.1103/physreve.84.011407openalex-snapshot
Interaction regimes for oppositely charged plates with multivalent counterions
inferred← citeshttps://doi.org/10.1103/physreve.97.022405openalex-snapshot
Effects of electrostatic interactions on ligand dissociation kinetics
inferred← citeshttps://doi.org/10.1103/physrevlett.102.228101openalex-snapshot
Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA
inferred← citeshttps://doi.org/10.1109/access.2019.2943748openalex-snapshot
InPrNa: A Tool for Insight Into Protein–Nucleic Acids Interaction Information
inferred← citeshttps://doi.org/10.1109/bibm.2012.6392699openalex-snapshot
Extending the ball-histogram method with continuous distributions and an application to prediction of DNA-binding proteins
inferred← citeshttps://doi.org/10.1109/bibm.2015.7359862openalex-snapshot
Mining graph patterns in the protein-RNA interfaces
inferred← citeshttps://doi.org/10.1109/bibm.2016.7822780openalex-snapshot
Mining structure patterns on the protein-DNA interfaces
inferred← citeshttps://doi.org/10.1109/bibm58861.2023.10385798openalex-snapshot
A Graph Method for Predicting Protein-RNA Interaction Using Reduced Amino Acid Alphabets
inferred← citeshttps://doi.org/10.1109/cibcb.2008.4675782openalex-snapshot
Mining sequence features for DNA-binding site prediction
inferred← citeshttps://doi.org/10.1109/cictn57981.2023.10141429openalex-snapshot
Prediction of DNA Interacting Residues
inferred← citeshttps://doi.org/10.1109/iembs.2005.1617004openalex-snapshot
Structure Based Prediction of Binding Residues on DNA-binding Proteins
inferred← citeshttps://doi.org/10.1109/ijcnn.2006.1716299openalex-snapshot
Comparing Kernels for Predicting Protein Binding Sites from Amino Acid Sequence
inferred← citeshttps://doi.org/10.1109/smc.2015.278openalex-snapshot
Data Analytics for Protein-DNA Binding Interactions
inferred← citeshttps://doi.org/10.1109/tcbb.2012.106openalex-snapshot
Sequence-Based Prediction of DNA-Binding Residues in Proteins with Conservation and Correlation Information
inferred← citeshttps://doi.org/10.1109/tcbb.2014.2343952openalex-snapshot
Discovering Binding Cores in Protein-DNA Binding Using Association Rule Mining with Statistical Measures
inferred← citeshttps://doi.org/10.1109/tcbb.2015.2474376openalex-snapshot
Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering
inferred← citeshttps://doi.org/10.1110/ps.04964705openalex-snapshot
A computational method for the analysis and prediction of protein:phosphopeptide‐binding sites
inferred← citeshttps://doi.org/10.1110/ps.073096508openalex-snapshot
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid
inferred← citeshttps://doi.org/10.1128/jb.00810-16openalex-snapshot
ThiN as a Versatile Domain of Transcriptional Repressors and Catalytic Enzymes of Thiamine Biosynthesis
inferred← citeshttps://doi.org/10.1128/jb.187.4.1455-1464.2005openalex-snapshot
DNA Binding: a Novel Function of Pseudomonas aeruginosa Type IV Pili
inferred← citeshttps://doi.org/10.1134/s0026893311040054openalex-snapshot
Machine learning study of DNA binding by transcription factors from the LacI family
inferred← citeshttps://doi.org/10.1142/s0219720006002387openalex-snapshot
PREDICTION OF DNA-BINDING RESIDUES FROM SEQUENCE FEATURES
inferred← citeshttps://doi.org/10.1186/1471-2105-13-s10-s3openalex-snapshot
Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search
inferred← citeshttps://doi.org/10.1186/1471-2105-7-262openalex-snapshot
Predicting DNA-binding sites of proteins from amino acid sequence
inferred← citeshttps://doi.org/10.1186/1471-2164-10-s3-s23openalex-snapshot
DNA-binding residues and binding mode prediction with binding-mechanism concerned models
inferred← citeshttps://doi.org/10.1186/1471-2229-10-14openalex-snapshot
SoyDB: a knowledge database of soybean transcription factors
inferred← citeshttps://doi.org/10.1186/1477-5956-10-66openalex-snapshot
Prediction of DNA-binding proteins from relational features
inferred← citeshttps://doi.org/10.1186/1752-0509-5-s1-s7openalex-snapshot
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction
inferred← citeshttps://doi.org/10.1186/1752-0509-8-s4-s10openalex-snapshot
A graph kernel method for DNA-binding site prediction
inferred← citeshttps://doi.org/10.1186/s12859-018-2527-1openalex-snapshot
PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine
inferred← citeshttps://doi.org/10.1186/s13065-023-00952-zopenalex-snapshot
Assessment of binding interaction to salmon sperm DNA of two antiviral agents and ecofriendly nanoparticles: comprehensive spectroscopic study
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000146openalex-snapshot
Classifying RNA-Binding Proteins Based on Electrostatic Properties
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000170openalex-snapshot
Insights into Protein–DNA Interactions through Structure Network Analysis
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000341openalex-snapshot
From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004639openalex-snapshot
A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007624openalex-snapshot
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties
inferred← citeshttps://doi.org/10.1371/journal.pone.0028440openalex-snapshot
Exploiting a Reduced Set of Weighted Average Features to Improve Prediction of DNA-Binding Residues from 3D Structures
inferred← citeshttps://doi.org/10.1371/journal.pone.0032647openalex-snapshot
On Docking, Scoring and Assessing Protein-DNA Complexes in a Rigid-Body Framework
inferred← citeshttps://doi.org/10.1371/journal.pone.0096694openalex-snapshot
Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome
inferred← citeshttps://doi.org/10.1371/journal.pone.0134954openalex-snapshot
The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation
inferred← citeshttps://doi.org/10.1371/journal.pone.0162681openalex-snapshot
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors
inferred← citeshttps://doi.org/10.1371/journal.pone.0174953openalex-snapshot
Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach
inferred← citeshttps://doi.org/10.21203/rs.3.rs-71923/v1openalex-snapshot
Binding mechanism of SARS-CoV-2 spike protein with human ACE2 receptor
inferred← citeshttps://doi.org/10.2172/836885openalex-snapshot
PROTEIN NUCLEIC ACID INTERACTIONS GRANT # DE-FG02-96ER62166 FINAL REPORT
inferred← citeshttps://doi.org/10.2174/092986610790780279openalex-snapshot
Improve the Prediction of RNA-Binding Residues Using Structural Neighbours
inferred← citeshttps://doi.org/10.26565/2075-3810-2017-38-06openalex-snapshot
Protein-DNA complexation: contact profiles in DNA grooves
inferred← citeshttps://doi.org/10.31274/etd-180810-4321openalex-snapshot
Protein-protein interface: database, analysis and prediction
inferred← citeshttps://doi.org/10.31274/rtd-180813-2240openalex-snapshot
Identification of interface residues involved in protein-protein and protein-DNA interactions from sequence using machine learning approaches
inferred← citeshttps://doi.org/10.3389/fgene.2018.00569openalex-snapshot
Comparative Analysis of Mycoplasma gallisepticum vlhA Promoters
inferred← citeshttps://doi.org/10.3389/fmolb.2022.978310openalex-snapshot
ProDFace: A web-tool for the dissection of protein-DNA interfaces
inferred← citeshttps://doi.org/10.3390/biom8030083openalex-snapshot
Molecular Modeling Applied to Nucleic Acid-Based Molecule Development
inferred← citeshttps://doi.org/10.3390/e18100379openalex-snapshot
A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence
inferred← citeshttps://doi.org/10.3390/ijms16035194openalex-snapshot
An Overview of the Prediction of Protein DNA-Binding Sites
inferred← citeshttps://doi.org/10.3390/ijms20051252openalex-snapshot
Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications
inferred← citeshttps://doi.org/10.3390/ijms24076315openalex-snapshot
Next Generation of Ovarian Cancer Detection Using Aptamers
inferred← citeshttps://doi.org/10.3923/tasr.2008.285.291openalex-snapshot
On the Accuracy of Sequence-Based Computational Inference of Protein Residues Involved in Interactions with DNA
inferred← citeshttps://doi.org/10.3934/mbe.2024008openalex-snapshot
Identification of DNA-protein binding residues through integration of Transformer encoder and Bi-directional Long Short-Term Memory
inferred← citeshttps://doi.org/10.48550/arxiv.1311.7496openalex-snapshot
Protein-DNA electrostatics: toward a new paradigm for protein sliding
inferred← citeshttps://doi.org/10.53846/goediss-3806openalex-snapshot
Molecular characterization of Mst77F and implication in Drosophila spermatogenesis
inferred← citeshttps://doi.org/10.53846/goediss-7595openalex-snapshot
Information theoretical approaches for the identification of potentially cooperating transcription factors
inferred← citeshttps://doi.org/10.53846/goediss-8461openalex-snapshot
Probabilistic Models to Detect Important Sites in Proteins
inferred← citeshttps://doi.org/10.70675/233e20e9zc3edz4785z8d11z871e7846fef9openalex-snapshot
Towards the in silico reconstruction of protein interaction networks : identification of DNA- and RNA-protein interfaces, and construction of a database of multiple interactions of proteins
inferred← citeshttps://doi.org/10.70675/6edd9acbz459az4f96zbd07z0886b7d73a41openalex-snapshot
Towards biocatalyst selection using microfluidically distributed molecular programs
inferred← citeshttps://doi.org/10.7554/elife.44993openalex-snapshot
Ion counting demonstrates a high electrostatic field generated by the nucleosome
inferred← citeshttps://doi.org/10.7912/c2/932openalex-snapshot
Protein function prediction by integrating sequence, structure and binding affinity information
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