Search

Showing total 111 results

Search Constraints

Start Over You searched for: Topic amino acids Remove constraint Topic: amino acids Journal plos computational biology Remove constraint Journal: plos computational biology Database Complementary Index Remove constraint Database: Complementary Index
111 results

Search Results

1. Bidirectional de novo peptide sequencing using a transformer model.

2. Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data.

3. Impact of phylogeny on the inference of functional sectors from protein sequence data.

4. The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.

5. Full-length ribosome density prediction by a multi-input and multi-output model.

6. Multi-state design of flexible proteins predicts sequences optimal for conformational change.

7. Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning.

8. Predicting B cell receptor substitution profiles using public repertoire data.

9. Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants.

10. Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.

11. Phylogenetic inference of changes in amino acid propensities with single-position resolution.

12. Comparison of metabolic states using genome-scale metabolic models.

13. Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel.

14. Computational design of substrate selective inhibition.

15. Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model.

16. Revealing evolutionary constraints on proteins through sequence analysis.

17. Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.

18. Motif-Aware PRALINE: Improving the alignment of motif regions.

19. All-atom normal mode dynamics of HIV-1 capsid.

20. Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics.

21. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.

22. Organization of the core respiratory network: Insights from optogenetic and modeling studies.

23. Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.

24. Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.

25. Identifying parameter regions for multistationarity.

26. A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect.

27. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile.

28. Protein charge distribution in proteomes and its impact on translation.

29. Exhaustive search of linear information encoding protein-peptide recognition.

30. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

31. Amino acid composition predicts prion activity.

32. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells.

33. Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

34. Exome Sequencing and Prediction of Long-Term Kidney Allograft Function.

35. Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

36. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

37. Evolution-Based Functional Decomposition of Proteins.

38. The Role of Adaptation in Bacterial Speed Races.

39. Non-degradative Ubiquitination of Protein Kinases.

40. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.

41. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

42. Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.

43. Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis.

44. Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation.

45. H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation.

46. Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection.

47. Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.

48. Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies.

49. Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes.

50. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.