Hoerschinger, V. J. | Search bioRxiv

bioRxiv2023

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity and Antibody Developability

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Due to their long-ranged nature, electrostatic interactions in proteins play a critical role in numerous processes, such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein is a pre-requisite for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface and showcase its applicability to elucidate protease substrate specificity, antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.

biophysics↗

bioRxiv2021

OCD.py - Characterizing immunoglobulin inter-domain orientations

SummaryInter-domain orientations between immunoglobulin domains are important for the modeling and engineering of novel antibody therapeutics. Previous tools to describe these orientations are applicable only to the variable domains of antibodies and T-cell receptors. We present the "Orientation of Cylindrical Domains (OCD)" tool, which employs a transferable approach to calculate inter-domain orientations for all immunoglobulin domains. Based on a reference structure, the OCD tool automatically builds a suitable reference coordinate system for each domain. Through alignment, the reference coordinate systems are transferred onto the sample to calculate six measures which fully characterize the inter-domain orientation. Availability and implementationThe OCD approach is implemented as a stand-alone Python script, OCD.py, which can handle multiple types of data input for the analysis of single structures and molecular dynamics trajectories alike. OCD.py is available at https://github.com/liedllab/OCD under MIT license. Supplementary InformationSupplementary information and data are available at Bioinformatics online.

bioinformatics↗