Simmerling C - Search Results

1

MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction.

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Patsahan T, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: simmerling c. Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011. Epub 2024 May 15. Biophys J. 2024. PMID: 38751115

2

Exact analytical algorithm for solvent accessible surface area and derivatives in implicit solvent molecular simulations on GPUs.

Cao X, Hummel MH, Wang Y, Simmerling C, Coutsias EA. Cao X, et al. Among authors: simmerling c. ArXiv [Preprint]. 2024 Apr 25:arXiv:2401.10462v2. ArXiv. 2024. Update in: J Chem Theory Comput. 2024 Jun 11;20(11):4456-4468. doi: 10.1021/acs.jctc.3c01366 PMID: 38313200 Free PMC article. Updated. Preprint.

3

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids.

Raguette LE, Cuomo AE, Belfon KAA, Tian C, Hazoglou V, Witek G, Telehany SM, Wu Q, Simmerling C. Raguette LE, et al. Among authors: simmerling c. J Chem Theory Comput. 2024 Aug 16. doi: 10.1021/acs.jctc.4c00732. Online ahead of print. J Chem Theory Comput. 2024. PMID: 39151116

4

Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations.

Raguette LE, Gunasekera SS, Diaz Ventura RI, Aminov E, Linzer JT, Parwana D, Wu Q, Simmerling C, Nagan MC. Raguette LE, et al. Among authors: simmerling c. J Phys Chem B. 2024 Aug 22;128(33):7921-7933. doi: 10.1021/acs.jpcb.4c01910. Epub 2024 Aug 7. J Phys Chem B. 2024. PMID: 39110091

5

Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein.

Stepanenko D, Wang Y, Simmerling C. Stepanenko D, et al. Among authors: simmerling c. Viruses. 2024 Jul 2;16(7):1066. doi: 10.3390/v16071066. Viruses. 2024. PMID: 39066230 Free PMC article.

6

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.

Linzer JT, Aminov E, Abdullah AS, Kirkup CE, Diaz Ventura RI, Bijoor VR, Jung J, Huang S, Tse CG, Álvarez Toucet E, Onghai HP, Ghosh AP, Grodzki AC, Haines ER, Iyer AS, Khalil MK, Leong AP, Neuhaus MA, Park J, Shahid A, Xie M, Ziembicki JM, Simmerling C, Nagan MC. Linzer JT, et al. Among authors: simmerling c. J Chem Inf Model. 2024 Aug 12;64(15):6092-6104. doi: 10.1021/acs.jcim.4c00756. Epub 2024 Jul 13. J Chem Inf Model. 2024. PMID: 39002142

7

k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations.

Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. Chen L, et al. Among authors: simmerling c. J Chem Theory Comput. 2024 Jul 9;20(13):5583-5597. doi: 10.1021/acs.jctc.4c00308. Epub 2024 Jun 21. J Chem Theory Comput. 2024. PMID: 38905589 Free PMC article.

8

Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.

Cao X, Hummel MH, Wang Y, Simmerling C, Coutsias EA. Cao X, et al. Among authors: simmerling c. J Chem Theory Comput. 2024 Jun 11;20(11):4456-4468. doi: 10.1021/acs.jctc.3c01366. Epub 2024 May 23. J Chem Theory Comput. 2024. PMID: 38780181

9

k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations.

Chen L, Roe DR, Kochert M, Simmerling C, Miranda-Quintana RA. Chen L, et al. Among authors: simmerling c. bioRxiv [Preprint]. 2024 Mar 8:2024.03.07.583975. doi: 10.1101/2024.03.07.583975. bioRxiv. 2024. Update in: J Chem Theory Comput. 2024 Jul 9;20(13):5583-5597. doi: 10.1021/acs.jctc.4c00308 PMID: 38496504 Free PMC article. Updated. Preprint.

10

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: simmerling c. bioRxiv [Preprint]. 2023 Dec 14:2023.11.29.569310. doi: 10.1101/2023.11.29.569310. bioRxiv. 2023. Update in: Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011 PMID: 38077000 Free PMC article. Updated. Preprint.

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