Algorithms for Computational Biology 2022

A special issue of Algorithms (ISSN 1999-4893). This special issue belongs to the section "Algorithms for Multidisciplinary Applications".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 2894

Special Issue Editor


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Guest Editor
Department of Computer and Communication Engineering, Ming Chuan University, 5 De Ming Road, Guishan District, Taoyuan City 333, Taiwan
Interests: design and analysis of algorithms; graph theory and combinatorial optimization; social network analysis; decision making; computational theory; operations research

Special Issue Information

Dear Colleagues, 

Computational biology is an extensive discipline that combines computational, statistical, experimental, and technological methods to build and analyze models for diverse biological data and systems. Many optimization problems have arisen from computational biology, such as biological sequence analysis, regulatory motif discovery, genome identification, and biochemical reaction networks. Computational biologists require fast algorithms to solve these optimization problems or a better understanding of complexity in the problems to help implement efficient solutions and design the concomitant high-performance computing and heuristic requirements. The principles and complexities of developing algorithms have been widely studied and analyzed for application to real biological data sets. The significance and implications of algorithms in computational biology are proliferating.

This Special Issue aims to improve our understanding of the interplay between algorithms and computational biology. The goal is to explore new directions in designing algorithms and establish new foundations in computational biology.

The scope of this Special Issue includes, but is not limited to:

  • The design and analysis of graph algorithms, randomized, parameterized, distributed, and other types of algorithms;
  • Biological sequence analysis, protein identification, regulatory motif discovery, evolutionary theory, clustering algorithms, and scale-free networks.

Dr. Chuan-Min Lee
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Algorithms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • algorithms
  • approximation algorithms
  • molecules
  • cells
  • tissues
  • organs

Published Papers (1 paper)

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Research

22 pages, 5465 KiB  
Article
Fast and Interactive Positioning of Proteins within Membranes
by André Lanrezac, Benoist Laurent, Hubert Santuz, Nicolas Férey and Marc Baaden
Algorithms 2022, 15(11), 415; https://doi.org/10.3390/a15110415 - 7 Nov 2022
Cited by 3 | Viewed by 2144
Abstract
(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an advanced molecular visualization software; MDDriver, a socket for data communication; [...] Read more.
(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an advanced molecular visualization software; MDDriver, a socket for data communication; and BioSpring, a Spring network simulation engine, were extended to perform IMS. These components are designed to easily communicate with each other, adapt to other molecular simulation software, and provide a development framework for adding new interaction models to simulate biological phenomena such as protein alignment in the membrane at a fast enough rate for real-time experiments. (3) Results: We describe in detail the integration of an implicit membrane model for Integral Membrane Protein And Lipid Association (IMPALA) into our IMS framework. Our implementation can cover multiple levels of representation, and the degrees of freedom can be tuned to optimize the experience. We explain the validation of this model in an interactive and exhaustive search mode. (4) Conclusions: Protein positioning in model membranes can now be performed interactively in real time. Full article
(This article belongs to the Special Issue Algorithms for Computational Biology 2022)
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