PeSA 2.0: A software tool for peptide specificity analysis implementing positive and negative motifs and motif-based peptide scoring

Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A

(2022) Anand Chopra et al.   Biomolecules

Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference

(2021) Matthew Hoekstra et al.   ANALYTICAL BIOCHEMISTRY

Applications of Protein Fragment Complementation Assays for Analyzing Biomolecular Interactions and Biochemical Networks in Living Cells

(2019) Peipei Li et al.   JOURNAL OF PROTEOME RESEARCH

PeSA: A software tool for peptide specificity analysis

(2019) Emine Topcu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach

(2016) Ashley J. Waardenberg et al.   Open Biology

Activity and specificity of the human SUV39H2 protein lysine methyltransferase

(2015) Maren Kirstin Schuhmacher et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Discovery of Substrates for a SET Domain Lysine Methyltransferase Predicted by Multistate Computational Protein Design

(2015) Sylvain Lanouette et al.   STRUCTURE

Substrate Specificity Analysis and Novel Substrates of the Protein Lysine Methyltransferase NSD1

(2014) Srikanth Kudithipudi et al.   CHEMISTRY & BIOLOGY

In silico prediction of physical protein interactions and characterization of interactome orphans

(2014) Max Kotlyar et al.   NATURE METHODS

A Method for Systematic Mapping of Protein Lysine Methylation Identifies Functions for HP1β in DNA Damage Response

(2013) Huadong Liu et al.   MOLECULAR CELL

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Prescont: Predicting protein-protein interfaces utilizing four residue properties

(2011) Hermann Zellner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach

(2008) Lei Li et al.   NUCLEIC ACIDS RESEARCH