Naujausi moksliniai straipsniai
ĮVADAS 
Čia pateikiame kruopščiai peržiūrėtus Folding@home projekto rezultatus. Norime pažymeti, kad norint publikuoti tokio lygio straipsnį moksliniuose žurnaluose (peer reviewed article), tenka kentėti nemažai laiko, kol tai visgi būna atspausdinta (dažnai tai trunka iki vienerių metų laiko). Kitas dalykas, tai straipsniai, skirti mokslininkams, todėl jums jie pasirodys labai techniški ir neįdomūs. Tačiau, šios publikacijos rodo mūsų pažangą, taip pat tai, kad jie viešai prieinami, ir dar nemažai straipsnių jau atiduoti spaudai ir greitai pasirodys.
(Straipsnių santrumpos angliškai, Papers)
Straipsnių sąrašas
(pirmieji straipsniai apačioje)
- 75. A simple theory of protein folding kinetics. - 74. Protein folded states are kinetic hubs. - 73. Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. - 72. Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39) - 71. Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint - 70. Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin. - 69. The Roles of Entropy and Kinetics in Structure Prediction. - 68. Using generalized ensemble simulations and Markov state models to identify conformational states. - 67. Folding@home: lessons from eight years of distributed computing. - 66. Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation. - 65. A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. - 64. The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations. - 63. Accelerating Molecular Dynamic Simulation on Graphics Processing Units. - 62. The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation - 61. Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. - 60. Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3 - 59. Side-chain recognition and gating in the ribosome exit tunnel - 58. Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach - 57. Structural Insight into RNA Hairpin Folding Intermediates - 56. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. - 55. N-Body simulation on GPUs - 54.Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics - 53. Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece - 52. Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics. - 51. Persistent voids: a new structural metric for membrane fusion. - 50. Protein folding under confinement: a role for solvent. - 49. Automatic State Decomposition Algorithm. - 48. Storage@home: Petascale Distributed Storage - 47. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide. - 46. A Bayesian Update Method for Adaptive Weighted Sampling. - 45. Local structure formation in simulations of two small proteins. - 44. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates. - 43. Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics. - 42. Folding Simulations of the Villin Headpiece in All-Atom Detail. - 41. Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion - 40. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory. - 39. A novel approach for computational alanine scanning: application to the p53 oligomerization domain. - 38. Validation of Markov state models using Shannon's entropy. - 37. On the role of chemical detail in simulating protein folding kinetics. - 36. Nanotube confinement denatures protein helices. - 35. The solvation interface is a determining factor in peptide conformational preferences. - 34. Can conformational change be described by only a few normal modes? - 33. How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD. - 32. Error Analysis in Markovian State Models for protein folding. - 31. Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer. - 30. A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides. - 29. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. - 28. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. - 27. Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. - 26. Foldamer dynamics expressed via Markov state models. II. State space decomposition. - 25. Unusual compactness of a polyproline type II structure. - 24. How well can simulation predict protein folding kinetics and thermodynamics? - 23. Empirical Force-Field Assessment: The Interplay Between Backbone Torsions and Noncovalent Term Scaling. - 22. Exploring the Helix-Coil Transition via All-atom Equilibrium Ensemble Simulations. - 21. Does Water Play a Structural Role in the Folding of Small Nucleic Acids? - 20. Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations. - 19. Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. - 18. Simulations of the role of water in the protein-folding mechanism. - 17. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. - 16. Does Native State Topology Determine the RNA Folding Mechanism? - 15. Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties. - 14. Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods. - 13. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. - 12. Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study. - 11. Insights Into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations. - 10. Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation. - 9. The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations. - 8. Absolute comparison of simulated and experimental protein-folding dynamics. - 7. Native-like Mean Structure in the Unfolded Ensemble of Small Proteins. - 6. Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwidedistributed Computing. - 5. Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology. - 4. Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing. - 3. b-Hairpin Folding Simulations in Atomistic Detail Using an Implicit Solvent Model. - 2. Mathematical Foundations of ensemble dynamics. - 1. Screen savers of the world, Unite!