Literature DB >> 26730484

Current updates on computer aided protein modeling and designing.

Faez Iqbal Khan1, Dong-Qing Wei1, Ke-Ren Gu1, Md Imtaiyaz Hassan2, Shams Tabrez3.   

Abstract

Determination of the three dimensional (3D) structure of a protein can provide important details about its biological functions and mechanism of action. However, despite their significance, the precise three-dimensional structures of most of the proteins are not fully determined till date. The main focus of the current review article is to gain a better understanding of the structural features of the proteins using computational techniques, and their relationship with function. Protein modeling and design is the method aimed to fold a primary amino acids sequence into protein structure with the ultimate goal of designing novel function and behavior. Moreover, proteins can also be designed from scratch or by similarity with the known protein structure. In the current article we have tried to cover various computer aided protein modeling and designing via homology and ab initio modeling, folding study using Molecular Dynamics (MD) methods and in silico mutation analysis.
Copyright © 2015 Elsevier B.V. All rights reserved.

Keywords:  In silico mutation analysis; Molecular dynamics simulations; Protein design; Protein modeling

Mesh:

Substances:

Year:  2015        PMID: 26730484     DOI: 10.1016/j.ijbiomac.2015.12.072

Source DB:  PubMed          Journal:  Int J Biol Macromol        ISSN: 0141-8130            Impact factor:   6.953


  22 in total

Review 1.  Harnessing glycoenzyme engineering for synthesis of bioactive oligosaccharides.

Authors:  Mounir Benkoulouche; Régis Fauré; Magali Remaud-Siméon; Claire Moulis; Isabelle André
Journal:  Interface Focus       Date:  2019-02-15       Impact factor: 3.906

Review 2.  Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.

Authors:  Mikhail N Ryazantsev; Dmitrii M Nikolaev; Andrey V Struts; Michael F Brown
Journal:  J Membr Biol       Date:  2019-09-30       Impact factor: 1.843

3.  Computer-Aided Design of α-L-Rhamnosidase to Increase the Synthesis Efficiency of Icariside I.

Authors:  Jia-Jun Huang; Hao-Xuan Hu; Yu-Jing Lu; Ya-Dan Bao; Jin-Lin Zhou; Mingtao Huang
Journal:  Front Bioeng Biotechnol       Date:  2022-06-21

4.  Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.

Authors:  Adam K Nijhawan; Arnold M Chan; Darren J Hsu; Lin X Chen; Kevin L Kohlstedt
Journal:  J Phys Chem B       Date:  2021-11-08       Impact factor: 3.466

5.  Structure and activation of the TSH receptor transmembrane domain.

Authors:  Ricardo Núñez Miguel; Jane Sanders; Jadwiga Furmaniak; Bernard Rees Smith
Journal:  Auto Immun Highlights       Date:  2016-12-05

6.  Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens.

Authors:  Fohad Mabood Husain; Iqbal Ahmad; Faez Iqbal Khan; Nasser A Al-Shabib; Mohammad Hassan Baig; Afzal Hussain; Md Tabish Rehman; Mohamed F Alajmi; Kevin A Lobb
Journal:  Front Cell Infect Microbiol       Date:  2018-10-25       Impact factor: 5.293

7.  In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine.

Authors:  Clara Carolina Silva De Oliveira; Gabriel Rodrigues Coutinho Pereira; Jamile Yvis Santos De Alcantara; Deborah Antunes; Ernesto Raul Caffarena; Joelma Freire De Mesquita
Journal:  PLoS One       Date:  2019-04-18       Impact factor: 3.240

8.  Remdesivir Strongly Binds to RNA-Dependent RNA Polymerase, Membrane Protein, and Main Protease of SARS-CoV-2: Indication From Molecular Modeling and Simulations.

Authors:  Faez Iqbal Khan; Tongzhou Kang; Haider Ali; Dakun Lai
Journal:  Front Pharmacol       Date:  2021-07-07       Impact factor: 5.988

9.  A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

Authors:  Dmitrii M Nikolaev; Andrey A Shtyrov; Maxim S Panov; Adeel Jamal; Oleg B Chakchir; Vladimir A Kochemirovsky; Massimo Olivucci; Mikhail N Ryazantsev
Journal:  ACS Omega       Date:  2018-07-09

10.  A Perspective on Thiazolidinone Scaffold Development as a New Therapeutic Strategy for Toxoplasmosis.

Authors:  Cristian Rocha-Roa; Diego Molina; Néstor Cardona
Journal:  Front Cell Infect Microbiol       Date:  2018-10-16       Impact factor: 5.293

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