Literature DB >> 33421906

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins.

Arvind Ramanathan1, Heng Ma2, Akash Parvatikar3, S Chakra Chennubhotla3.   

Abstract

We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships-however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Year:  2021        PMID: 33421906     DOI: 10.1016/j.sbi.2020.12.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  7 in total

1.  Artificial intelligence guided conformational mining of intrinsically disordered proteins.

Authors:  Aayush Gupta; Souvik Dey; Alan Hicks; Huan-Xiang Zhou
Journal:  Commun Biol       Date:  2022-06-20

Review 2.  Intrinsically Disordered Proteins: Critical Components of the Wetware.

Authors:  Prakash Kulkarni; Supriyo Bhattacharya; Srisairam Achuthan; Amita Behal; Mohit Kumar Jolly; Sourabh Kotnala; Atish Mohanty; Govindan Rangarajan; Ravi Salgia; Vladimir Uversky
Journal:  Chem Rev       Date:  2022-02-16       Impact factor: 72.087

3.  AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Authors:  Mihaly Varadi; Stephen Anyango; Mandar Deshpande; Sreenath Nair; Cindy Natassia; Galabina Yordanova; David Yuan; Oana Stroe; Gemma Wood; Agata Laydon; Augustin Žídek; Tim Green; Kathryn Tunyasuvunakool; Stig Petersen; John Jumper; Ellen Clancy; Richard Green; Ankur Vora; Mira Lutfi; Michael Figurnov; Andrew Cowie; Nicole Hobbs; Pushmeet Kohli; Gerard Kleywegt; Ewan Birney; Demis Hassabis; Sameer Velankar
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 19.160

4.  PDBe-KB: collaboratively defining the biological context of structural data.

Authors: 
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

Review 5.  When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.

Authors:  Sophie Sacquin-Mora; Chantal Prévost
Journal:  Biomolecules       Date:  2021-10-16

6.  IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.

Authors:  João M C Teixeira; Zi Hao Liu; Ashley Namini; Jie Li; Robert M Vernon; Mickaël Krzeminski; Alaa A Shamandy; Oufan Zhang; Mojtaba Haghighatlari; Lei Yu; Teresa Head-Gordon; Julie D Forman-Kay
Journal:  J Phys Chem A       Date:  2022-08-28       Impact factor: 2.944

Review 7.  AlphaFold, Artificial Intelligence (AI), and Allostery.

Authors:  Ruth Nussinov; Mingzhen Zhang; Yonglan Liu; Hyunbum Jang
Journal:  J Phys Chem B       Date:  2022-08-17       Impact factor: 3.466

  7 in total

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