121 related articles for article (PubMed ID: 33400654)
1. Improved Protein Decoy Selection via Non-Negative Matrix Factorization.
Akhter N; Kabir KL; Chennupati G; Vangara R; Alexandrov BS; Djidjev H; Shehu A
IEEE/ACM Trans Comput Biol Bioinform; 2022; 19(3):1670-1682. PubMed ID: 33400654
[TBL] [Abstract][Full Text] [Related]
2. Decoy selection for protein structure prediction via extreme gradient boosting and ranking.
Akhter N; Chennupati G; Djidjev H; Shehu A
BMC Bioinformatics; 2020 Dec; 21(Suppl 1):189. PubMed ID: 33297949
[TBL] [Abstract][Full Text] [Related]
3. From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.
Akhter N; Shehu A
Molecules; 2018 Jan; 23(1):. PubMed ID: 29351266
[TBL] [Abstract][Full Text] [Related]
4. Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction.
Zaman AB; Shehu A
BMC Bioinformatics; 2019 Apr; 20(1):211. PubMed ID: 31023237
[TBL] [Abstract][Full Text] [Related]
5. Unsupervised multi-instance learning for protein structure determination.
Alam FF; Shehu A
J Bioinform Comput Biol; 2021 Feb; 19(1):2140002. PubMed ID: 33568002
[TBL] [Abstract][Full Text] [Related]
6. An improved method to detect correct protein folds using partial clustering.
Zhou J; Wishart DS
BMC Bioinformatics; 2013 Jan; 14():11. PubMed ID: 23323835
[TBL] [Abstract][Full Text] [Related]
7. Entropy-accelerated exact clustering of protein decoys.
Berenger F; Zhou Y; Shrestha R; Zhang KY
Bioinformatics; 2011 Apr; 27(7):939-45. PubMed ID: 21310747
[TBL] [Abstract][Full Text] [Related]
8. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.
Chae MH; Krull F; Knapp EW
Proteins; 2015 May; 83(5):881-90. PubMed ID: 25693513
[TBL] [Abstract][Full Text] [Related]
9. How well can we predict native contacts in proteins based on decoy structures and their energies?
Zhu J; Zhu Q; Shi Y; Liu H
Proteins; 2003 Sep; 52(4):598-608. PubMed ID: 12910459
[TBL] [Abstract][Full Text] [Related]
10. Calibur: a tool for clustering large numbers of protein decoys.
Li SC; Ng YK
BMC Bioinformatics; 2010 Jan; 11():25. PubMed ID: 20070892
[TBL] [Abstract][Full Text] [Related]
11. Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction.
Akhter N; Hassan L; Rajabi Z; Barbará D; Shehu A
Methods Mol Biol; 2019; 1958():147-171. PubMed ID: 30945218
[TBL] [Abstract][Full Text] [Related]
12. Amino acid network for the discrimination of native protein structures from decoys.
Zhou J; Yan W; Hu G; Shen B
Curr Protein Pept Sci; 2014; 15(6):522-8. PubMed ID: 25059328
[TBL] [Abstract][Full Text] [Related]
13. Network properties of protein-decoy structures.
Chatterjee S; Bhattacharyya M; Vishveshwara S
J Biomol Struct Dyn; 2012; 29(6):606-22. PubMed ID: 22545992
[TBL] [Abstract][Full Text] [Related]
14. SVR_CAF: an integrated score function for detecting native protein structures among decoys.
Zhou J; Yan W; Hu G; Shen B
Proteins; 2014 Apr; 82(4):556-64. PubMed ID: 24115148
[TBL] [Abstract][Full Text] [Related]
15. 3DRobot: automated generation of diverse and well-packed protein structure decoys.
Deng H; Jia Y; Zhang Y
Bioinformatics; 2016 Feb; 32(3):378-87. PubMed ID: 26471454
[TBL] [Abstract][Full Text] [Related]
16. evERdock BAI: Machine-learning-guided selection of protein-protein complex structure.
Terayama K; Shinobu A; Tsuda K; Takemura K; Kitao A
J Chem Phys; 2019 Dec; 151(21):215104. PubMed ID: 31822094
[TBL] [Abstract][Full Text] [Related]
17. Consensus scoring for enriching near-native structures from protein-protein docking decoys.
Liang S; Meroueh SO; Wang G; Qiu C; Zhou Y
Proteins; 2009 May; 75(2):397-403. PubMed ID: 18831053
[TBL] [Abstract][Full Text] [Related]
18. Reliable Generation of Native-Like Decoys Limits Predictive Ability in Fragment-Based Protein Structure Prediction.
Kandathil SM; Garza-Fabre M; Handl J; Lovell SC
Biomolecules; 2019 Oct; 9(10):. PubMed ID: 31618996
[TBL] [Abstract][Full Text] [Related]
19. Ranking near-native candidate protein structures via random forest classification.
Wu H; Huang H; Lu W; Fu Q; Ding Y; Qiu J; Li H
BMC Bioinformatics; 2019 Dec; 20(Suppl 25):683. PubMed ID: 31874596
[TBL] [Abstract][Full Text] [Related]
20. SPICKER: a clustering approach to identify near-native protein folds.
Zhang Y; Skolnick J
J Comput Chem; 2004 Apr; 25(6):865-71. PubMed ID: 15011258
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
