About this App (version 1.0)

The Ceff Calculator is a platform-independent browser-based interface that facilitates the analysis of flexible linker properties by applying the worm like chain model (WLC model). The application allows the analysis of effective concentrations enforced by linkers and of linker dimensions represented as the probability distribution of end-to-end distances. The application requires the user to define the system specific parameters and allows an easy access to important parameters such as the optimal linker length for maximal enhancement of avidity and the effective concentration at a specific linker length. These features help in protein design for biotechnology applications and also in the analysis of biological systems.

The Ceff Calculator was developed by the @ChemesLab. The application is based on the Shiny package and it was coded by Juliana Glavina, PhD, with server implementation by Cesar Leonetti.

Please, report problems, questions and feedback on the app to support@chemeslab.org.

The use of the Ceff Calculator is described in detail in Kjaergaard M, Glavina J and Chemes LB. Predicting the effect of disordered linkers on effective concentrations and avidity with the “Ceff calculator” app (see References tab). This page briefly outlines how to use this app and the theory behind the calculations. It's organized in the following main sections:

Before you start

The first step towards calculating effective concentrations is to determine the length of the linker and the spacing between binding sites in your system. Here, we briefly outline how to identify these two parameters. For further details, see Kjaergaard M et al. 2020 in the References tab.

Mapping linker boundaries

The mapping of linker boundaries depends on what the linker is connected to. For folded domains with a known 3D structure the linker starts at the first or last residue that is not resolved in the structure. If there is no structure, you can predict conserved domains using CDD or PFAM in combination with a disorder predictor such as MobiDB, which collates the consensus of different predictors, or a single predictor such as MFDp2 to define linker boundaries. If the linker tethers a short linear motif, the linker can usually be assumed to start after the last residue of the motif, or end the first residue before the start of the motif.

Measuring the distance between sites

Intramolecular and multivalent interactions are also modulated by the distance separating the attachment sites of the linker, named ro in the model. For intramolecular binding, the distance between contact sites is that between the linker attachment site and the binding site. In a bivalent interaction, the relevant distance is the distance between binding sites. If the 3D structure of the complex is available from the Protein Data Bank, you can use a program for visualization and analysis of protein structures, such as Chimera and PyMol and measure the distance between contact sites.

Ceff Plot Tab

The Ceff Plot Tab (FIG. 1) allows the visualization of effective concentration (Ceff) as a function of linker length for a thethered system.