ArticleNucleic acids research2007
Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 59 citations in OpenAlex.
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- PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.Journal of chemical information and modeling · 2023Article
- Protein-RNA interaction prediction with deep learning: structure matters.Briefings in bioinformatics · 2022Article
- CHD4 Conceals Aberrant CTCF-Binding Sites at TAD Interiors by Regulating Chromatin Accessibility in Mouse Embryonic Stem Cells.Molecules and cells · 2021Article
- Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins.Nature communications · 2021Article
- Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation.International journal of molecular sciences · 2019Review
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
- Argonaute 8 (AGO8) Mediates the Elicitation of Direct Defenses against Herbivory.Plant physiology · 2017Article
- Genome-wide characterization of cellulases from the hemi-biotrophic plant pathogen,Biotechnology for biofuels · 2017Article
- RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.Nucleic acids research · 2016Article
- BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.Nucleic acids research · 2016Article
- Computational Prediction of RNA-Binding Proteins and Binding Sites.International journal of molecular sciences · 2015Review
- RNA-binding residues prediction using structural features.BMC bioinformatics · 2015Article
- Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score.Nucleic acids research · 2015Article
- An overview of the prediction of protein DNA-binding sites.International journal of molecular sciences · 2015Review
- Article
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- DBSI: DNA-binding site identifier.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.