Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus

Tekpinar M., Neron B., Delarue M.

Journal of Chemical Information and Modeling, cilt.61, sa.10, ss.4832-4838, 2021 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 61 Sayı: 10
  • Basım Tarihi: 2021
  • Doi Numarası: 10.1021/acs.jcim.1c00742
  • Dergi Adı: Journal of Chemical Information and Modeling
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Applied Science & Technology Source, Compendex, Computer & Applied Sciences, EMBASE, MEDLINE
  • Sayfa Sayıları: ss.4832-4838
  • Van Yüzüncü Yıl Üniversitesi Adresli: Evet

Özet

Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions. Efficient and flexible tools to perform this task can provide new insights about residues involved in allosteric regulation and protein function. In addition, combining and comparing dynamical coupling information with sequence coevolution data can help to understand better protein function. To this aim, we developed a Python package called correlationplus to calculate, visualize, and analyze pairwise correlations. In this way, the package aids to identify key residues and interactions in proteins. The source code of correlationplus is available under LGPL version 3 at https://github.com/tekpinar/correlationplus. The current version of the package (0.2.0) can be installed with common installation methods like conda or pip in addition to source code installation. Moreover, docker images are also available for usage of the code without installation.