GeVaDSs – decision support system for novel Genetic Vaccine development process

Błażewicz, Jacek; Borowski, Marcin; Chaara, Wahiba; Kędziora, Patrycja; Klatzmann, David; Łukasiak, Piotr; Six, Adrien; Wojciechowski, Pawel

doi:10.1186/1471-2105-13-91

Cited by 5 publications

(2 citation statements)

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“…For example, there exist excellent software tools for analyzing gene-regulatory or biochemical networks CellDesigner [ 2 ], COPASI [ 3 ], The Cell Collective [ 4 ], and SimBiology [ 5 ]. However, in some areas, such as viral infection modelin [ 6 , 7 ], there is still a possibility to improve existing tools.…”

Section: Introductionmentioning

confidence: 99%

ModeLang: A New Approach for Experts-Friendly Viral Infections Modeling

Wasik

Prejzendanc

Błażewicz

2013

Computational and Mathematical Methods in Medicine

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Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces communication problems because biologists do not have sufficient knowledge to understand mathematical description of the models, and mathematicians do not have sufficient knowledge to define and verify these models. In many areas of systems biology, this problem has already been solved; however, in some of these areas there are still certain problematic aspects. The goal of the presented research was to facilitate this cooperation by designing seminatural formal language for describing viral infection models that will be easy to understand for biologists and easy to use by mathematicians and computer scientists. The ModeLang language was designed in cooperation with biologists and its computer implementation was prepared. Tests proved that it can be successfully used to describe commonly used viral infection models and then to simulate and verify them. As a result, it can make cooperation between biologists and mathematicians modeling viral infections much easier, speeding up computational verification of formulated hypotheses.

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Section: Introductionmentioning

confidence: 99%

ModeLang: A New Approach for Experts-Friendly Viral Infections Modeling

Wasik

Prejzendanc

Błażewicz

2013

Computational and Mathematical Methods in Medicine

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“…One of the consequences of recognizing a DNA sequence of a gene is an attempt to determine the corresponding 3D protein structure. Understanding the process of protein folding is crucial for human health (e.g., drug design, vaccination [ 2 ]), because its tertiary structure strictly determines its biological activity in a cell. Over the years, several computational techniques were proposed for predicting secondary [ 3 ] and tertiary structures of proteins [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

Structural alignment of protein descriptors – a combinatorial model

et al. 2016

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BackgroundStructural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction.ResultsIn this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency.ConclusionsAll the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare descriptors of biological molecules, such as proteins and RNAs. Both PDB (Protein Data Bank) and mmCIF (macromolecular Crystallographic Information File) formats are supported. The proposed tool is available as an open source project stored on GitHub (https://github.com/mantczak/descs-standalone).Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1237-9) contains supplementary material, which is available to authorized users.

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