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 *

131 related articles for article (PubMed ID: 37387189)

  • 1. Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles.
    Amarasinghe PR; Allison L; Stuckey PJ; Garcia de la Banda M; Lesk AM; Konagurthu AS
    Bioinformatics; 2023 Jun; 39(39 Suppl 1):i357-i367. PubMed ID: 37387189
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.
    Mortensen JC; Damjanovic J; Miao J; Hui T; Lin YS
    Protein Sci; 2022 Dec; 31(12):e4491. PubMed ID: 36327064
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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]  

  • 4. 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]  

  • 5. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains.
    Dunbrack RL; Karplus M
    Nat Struct Biol; 1994 May; 1(5):334-40. PubMed ID: 7664040
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks.
    Helles G; Fonseca R
    BMC Bioinformatics; 2009 Oct; 10():338. PubMed ID: 19835576
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors.
    Sumanaweera D; Allison L; Konagurthu AS
    Bioinformatics; 2019 Jul; 35(14):i360-i369. PubMed ID: 31510703
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures.
    Konagurthu AS; Subramanian R; Allison L; Abramson D; de la Banda MG; Stuckey PJ; Lesk AM
    Methods Mol Biol; 2019; 1958():123-131. PubMed ID: 30945216
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Equilibrium transitions between side-chain conformations in leucine and isoleucine.
    Caballero D; Smith WW; O'Hern CS; Regan L
    Proteins; 2015 Aug; 83(8):1488-99. PubMed ID: 26018846
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Revisiting the Ramachandran plot from a new angle.
    Zhou AQ; O'Hern CS; Regan L
    Protein Sci; 2011 Jul; 20(7):1166-71. PubMed ID: 21538644
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.
    Broz M; Jukič M; Bren U
    Molecules; 2023 Oct; 28(20):. PubMed ID: 37894526
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Antibody side chain conformations are position-dependent.
    Leem J; Georges G; Shi J; Deane CM
    Proteins; 2018 Apr; 86(4):383-392. PubMed ID: 29318667
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Prediction of disulfide dihedral angles using chemical shifts.
    Armstrong DA; Kaas Q; Rosengren KJ
    Chem Sci; 2018 Aug; 9(31):6548-6556. PubMed ID: 30310586
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Using information theory to discover side chain rotamer classes: analysis of the effects of local backbone structure.
    Fetrow JS; Berg G
    Pac Symp Biocomput; 1999; ():278-89. PubMed ID: 10380204
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Advantages of fine-grained side chain conformer libraries.
    Shetty RP; De Bakker PI; DePristo MA; Blundell TL
    Protein Eng; 2003 Dec; 16(12):963-9. PubMed ID: 14983076
    [TBL] [Abstract][Full Text] [Related]  

  • 16. New insights into the interdependence between amino acid stereochemistry and protein structure.
    Zhou AQ; Caballero D; O'Hern CS; Regan L
    Biophys J; 2013 Nov; 105(10):2403-11. PubMed ID: 24268152
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.
    Boomsma W; Hamelryck T
    BMC Bioinformatics; 2005 Jun; 6():159. PubMed ID: 15985178
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.
    Kirys T; Ruvinsky AM; Tuzikov AV; Vakser IA
    Proteins; 2012 Aug; 80(8):2089-98. PubMed ID: 22544766
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Prediction of backbone dihedral angles and protein secondary structure using support vector machines.
    Kountouris P; Hirst JD
    BMC Bioinformatics; 2009 Dec; 10():437. PubMed ID: 20025785
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Circular clustering of protein dihedral angles by Minimum Message Length.
    Dowe DL; Allison L; Dix TI; Hunter L; Wallace CS; Edgoose T
    Pac Symp Biocomput; 1996; ():242-55. PubMed ID: 9390236
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.