Literature DB >> 30853739

Protein structure prediction.

Haiyou Deng1, Ya Jia2, Yang Zhang3.   

Abstract

Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.

Entities:  

Keywords:  Protein structure prediction; ab initio prediction; homology modeling; structure refinement

Year:  2017        PMID: 30853739      PMCID: PMC6407873          DOI: 10.1142/S021797921840009X

Source DB:  PubMed          Journal:  Int J Mod Phys B        ISSN: 0217-9792            Impact factor:   1.219


  63 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-04-09       Impact factor: 5.469

3.  Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction.

Authors:  R Samudrala; M Levitt
Journal:  Protein Sci       Date:  2000-07       Impact factor: 6.725

4.  A distance-dependent atomic knowledge-based potential for improved protein structure selection.

Authors:  H Lu; J Skolnick
Journal:  Proteins       Date:  2001-08-15

5.  TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

Authors:  D Kihara; H Lu; A Kolinski; J Skolnick
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-14       Impact factor: 11.205

6.  Predicting novel protein folds by using FRAGFOLD.

Authors:  D T Jones
Journal:  Proteins       Date:  2001

Review 7.  New Monte Carlo algorithms for protein folding.

Authors:  U H Hansmann; Y Okamoto
Journal:  Curr Opin Struct Biol       Date:  1999-04       Impact factor: 6.809

8.  Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.

Authors:  Hongyi Zhou; Yaoqi Zhou
Journal:  Protein Sci       Date:  2002-11       Impact factor: 6.725

9.  Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.

Authors:  S Tanaka; H A Scheraga
Journal:  Macromolecules       Date:  1976 Nov-Dec       Impact factor: 5.985

10.  Replica Monte Carlo simulation of spin glasses.

Authors: 
Journal:  Phys Rev Lett       Date:  1986-11-24       Impact factor: 9.161

View more
  11 in total

1.  The molecular nature of the 17β-Estradiol binding site in the voltage- and Ca2+-activated K+ (BK) channel β1 subunit.

Authors:  Sara T Granados; Karen Castillo; Felipe Bravo-Moraga; Romina V Sepúlveda; Willy Carrasquel-Ursulaez; Maximiliano Rojas; Emerson Carmona; Yenisleidy Lorenzo-Ceballos; Fernando González-Nilo; Carlos González; Ramón Latorre; Yolima P Torres
Journal:  Sci Rep       Date:  2019-07-10       Impact factor: 4.379

Review 2.  The Application of Artificial Intelligence in the Genetic Study of Alzheimer's Disease.

Authors:  Rohan Mishra; Bin Li
Journal:  Aging Dis       Date:  2020-12-01       Impact factor: 6.745

3.  Enhancing protein inter-residue real distance prediction by scrutinising deep learning models.

Authors:  Julia Rahman; M A Hakim Newton; Md Khaled Ben Islam; Abdul Sattar
Journal:  Sci Rep       Date:  2022-01-17       Impact factor: 4.379

Review 4.  Graph representation learning for structural proteomics.

Authors:  Romanos Fasoulis; Georgios Paliouras; Lydia E Kavraki
Journal:  Emerg Top Life Sci       Date:  2021-12-21

Review 5.  Current Approaches in Supersecondary Structures Investigation.

Authors:  Vladimir R Rudnev; Liudmila I Kulikova; Kirill S Nikolsky; Kristina A Malsagova; Arthur T Kopylov; Anna L Kaysheva
Journal:  Int J Mol Sci       Date:  2021-11-02       Impact factor: 5.923

Review 6.  Deep learning tools for advancing drug discovery and development.

Authors:  Sagorika Nag; Anurag T K Baidya; Abhimanyu Mandal; Alen T Mathew; Bhanuranjan Das; Bharti Devi; Rajnish Kumar
Journal:  3 Biotech       Date:  2022-04-09       Impact factor: 2.893

Review 7.  A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level.

Authors:  Nan Ye; Feng Zhou; Xingchen Liang; Haiting Chai; Jianwei Fan; Bo Li; Jian Zhang
Journal:  Biomed Res Int       Date:  2022-03-31       Impact factor: 3.411

Review 8.  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

9.  A Divergent Articulavirus in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons.

Authors:  Ayda Susana Ortiz-Baez; John-Sebastian Eden; Craig Moritz; Edward C Holmes
Journal:  Viruses       Date:  2020-06-04       Impact factor: 5.048

10.  Simple Selection Procedure to Distinguish between Static and Flexible Loops.

Authors:  Karolina Mitusińska; Tomasz Skalski; Artur Góra
Journal:  Int J Mol Sci       Date:  2020-03-26       Impact factor: 5.923

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.