These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

218 related articles for article (PubMed ID: 22072531)

  • 1. SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.
    Nagata K; Randall A; Baldi P
    Proteins; 2012 Jan; 80(1):142-53. PubMed ID: 22072531
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures.
    Nagata K; Randall A; Baldi P
    Bioinformatics; 2014 Jun; 30(12):1681-9. PubMed ID: 24574112
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.
    Mendes J; Nagarajaram HA; Soares CM; Blundell TL; Carrondo MA
    Biopolymers; 2001 Aug; 59(2):72-86. PubMed ID: 11373721
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Protein side-chain modeling with a protein-dependent optimized rotamer library.
    Francis-Lyon P; Koehl P
    Proteins; 2014 Sep; 82(9):2000-17. PubMed ID: 24623614
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Improved prediction of protein side-chain conformations with SCWRL4.
    Krivov GG; Shapovalov MV; Dunbrack RL
    Proteins; 2009 Dec; 77(4):778-95. PubMed ID: 19603484
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Improved modeling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.
    Mendes J; Baptista AM; Carrondo MA; Soares CM
    Proteins; 1999 Dec; 37(4):530-43. PubMed ID: 10651269
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Improved packing of protein side chains with parallel ant colonies.
    Quan L; Lü Q; Li H; Xia X; Wu H
    BMC Bioinformatics; 2014; 15 Suppl 12(Suppl 12):S5. PubMed ID: 25474164
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Side-chain modeling with an optimized scoring function.
    Liang S; Grishin NV
    Protein Sci; 2002 Feb; 11(2):322-31. PubMed ID: 11790842
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Statistically based reduced representation of amino acid side chains.
    Rainey JK; Goh MC
    J Chem Inf Comput Sci; 2004; 44(3):817-30. PubMed ID: 15154746
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.
    Huang X; Pearce R; Zhang Y
    J Chem Inf Model; 2020 Jan; 60(1):410-420. PubMed ID: 31851497
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Deep architectures for protein contact map prediction.
    Di Lena P; Nagata K; Baldi P
    Bioinformatics; 2012 Oct; 28(19):2449-57. PubMed ID: 22847931
    [TBL] [Abstract][Full Text] [Related]  

  • 12. A protein-dependent side-chain rotamer library.
    Bhuyan MS; Gao X
    BMC Bioinformatics; 2011 Dec; 12 Suppl 14(Suppl 14):S10. PubMed ID: 22373394
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Prediction and evaluation of side-chain conformations for protein backbone structures.
    Shenkin PS; Farid H; Fetrow JS
    Proteins; 1996 Nov; 26(3):323-52. PubMed ID: 8953653
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.
    Shapovalov MV; Dunbrack RL
    Structure; 2011 Jun; 19(6):844-58. PubMed ID: 21645855
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Protein side chain conformation predictions with an MMGBSA energy function.
    Gaillard T; Panel N; Simonson T
    Proteins; 2016 Jun; 84(6):803-19. PubMed ID: 26948696
    [TBL] [Abstract][Full Text] [Related]  

  • 16. OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.
    Xu G; Wang Q; Ma J
    J Chem Inf Model; 2020 Dec; 60(12):6691-6697. PubMed ID: 33211480
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
    Bower MJ; Cohen FE; Dunbrack RL
    J Mol Biol; 1997 Apr; 267(5):1268-82. PubMed ID: 9150411
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Protein design using continuous rotamers.
    Gainza P; Roberts KE; Donald BR
    PLoS Comput Biol; 2012 Jan; 8(1):e1002335. PubMed ID: 22279426
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.
    Renfrew PD; Butterfoss GL; Kuhlman B
    Proteins; 2008 Jun; 71(4):1637-46. PubMed ID: 18076032
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.
    Peterson RW; Dutton PL; Wand AJ
    Protein Sci; 2004 Mar; 13(3):735-51. PubMed ID: 14978310
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.