Introducing VIKING: A Novel Online Platform for Multiscale Modeling

Abstract

Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.

Frontiers in Multiscale Modeling of Photoreceptor Proteins

“…Computational protocols for multiscale modeling of photoreceptor proteins involve a large number of computer programs and protocols that are highly specialized for a particular modeling technique and scale of modeling (171) The new platform VIKING (Scandina vi an Online Ki t for N anoscale Modellin g , viking‐suite.com) integrates a number of these tools in a single easy‐to‐use multiscale platform, which provides tools for setting up simulations, data analysis and visualization (172) VIKING alleviates the need for specialized know‐how, which is traditionally required for each individual modeling technique, and also provides a standardized workflow, making the elaborate work of integrating multiple methods in a single study significantly more tractable and reproducible. The primary goal of VIKING is to deliver a set of standard protocols, which researchers can use to study complex functioning of biomolecular systems, such as photoreceptors.…”

Introducing Pep McConst—A user‐friendly peptide modeler for biophysical applications

“…P ep McConst has been linked to VIKING 16 to permit constructing polypeptide chains, as a new stand‐alone procedure in the framework of the platform. VIKING provides a web‐based interface for configuring computational tasks.…”

“…Significant attention is devoted to check for the robustness of the emerging structure, which depending on the length and the considered residue types can become computationally demanding. In order to provide a user‐friendly approach, the software has been incorporated into the Scandinavian Online Kit for Nanoscale Modeling (VIKING) platform, http://viking-suite.com 16 …”

Modeling the Energy Landscape of Side Reactions in the Cytochrome bc1 Complex

“…Studying complex biomolecular processes computationally generally require a range of computational modeling tools covering different time and length scales (Korol et al, 2020). The present work employs several computational modeling FIGURE 1 | The bc 1 complex and its reaction cycle.…”

“…Studying complex biomolecular processes computationally generally require a range of computational modeling tools covering different time and length scales ( Korol et al, 2020 ). The present work employs several computational modeling techniques at both the quantum and classical level to characterize the possible reactions leading to superoxide formation at the Q o -site of the complex.…”