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Literature DB >> 31363226

Promoting transparency and reproducibility in enhanced molecular simulations.

Abstract

Mesh：

Year: 2019 PMID： 31363226 DOI： 10.1038/s41592-019-0506-8

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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71 in total

1. Neural networks-based variationally enhanced sampling.

Authors: Luigi Bonati; Yue-Yu Zhang; Michele Parrinello
Journal: Proc Natl Acad Sci U S A Date: 2019-08-15 Impact factor: 11.205

2. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.

Authors: Elin Karlsson; Cristina Paissoni; Amanda M Erkelens; Zeinab A Tehranizadeh; Frieda A Sorgenfrei; Eva Andersson; Weihua Ye; Carlo Camilloni; Per Jemth
Journal: J Biol Chem Date: 2020-10-16 Impact factor: 5.157

3. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution.

Authors: Benedetta Maria Sala; Tanguy Le Marchand; Guido Pintacuda; Carlo Camilloni; Antonino Natalello; Stefano Ricagno
Journal: Biophys J Date: 2020-07-24 Impact factor: 4.033

4. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria.

Authors: Rachael A Mansbach; Inga V Leus; Jitender Mehla; Cesar A Lopez; John K Walker; Valentin V Rybenkov; Nicolas W Hengartner; Helen I Zgurskaya; S Gnanakaran
Journal: J Chem Inf Model Date: 2020-06-09 Impact factor: 4.956

5. Impact of Glutamate Carboxylation in the Adsorption of the α-1 Domain of Osteocalcin to Hydroxyapatite and Titania.

Authors: Sarah Alamdari; Jim Pfaendtner
Journal: Mol Syst Des Eng Date: 2019-12-09

6. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.

Authors: Laura C Watkins; William F DeGrado; Gregory A Voth
Journal: J Am Chem Soc Date: 2022-01-05 Impact factor: 15.419

Promoting transparency and reproducibility in enhanced molecular simulations.

1. Neural networks-based variationally enhanced sampling.

2. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.

3. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution.

4. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria.

5. Impact of Glutamate Carboxylation in the Adsorption of the α-1 Domain of Osteocalcin to Hydroxyapatite and Titania.

6. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.

7. Transient exposure of a buried phosphorylation site in an autoinhibited protein.

Review 8. Ab Initio Machine Learning in Chemical Compound Space.

9. Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.

10. Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods.