Carlos Simmerling
Overview
Explore the profile of Carlos Simmerling including associated specialties, affiliations and a list of published articles.
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101
Citations
12701
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Recent Articles
1.
Mikulska-Ruminska K, Krieger J, Banerjee A, Cao X, Wu G, Bogetti A, et al.
J Mol Biol
. 2025 Feb;
:169009.
PMID: 39954779
ProDy is a widely used application programming interface for analyzing the collective dynamics of proteins and their complexes, offering enhanced capabilities to address the growing needs of the computational biology...
2.
Raguette L, Cuomo A, Belfon K, Tian C, Hazoglou V, Witek G, et al.
J Chem Theory Comput
. 2024 Aug;
PMID: 39151116
Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range...
3.
Raguette L, Gunasekera S, Diaz Ventura R, Aminov E, Linzer J, Parwana D, et al.
J Phys Chem B
. 2024 Aug;
128(33):7921-7933.
PMID: 39110091
The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how...
4.
Stepanenko D, Wang Y, Simmerling C
Viruses
. 2024 Jul;
16(7).
PMID: 39066230
One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions, the fusion peptide proximal region (FPPR) of...
5.
Linzer J, Aminov E, Abdullah A, Kirkup C, Diaz Ventura R, Bijoor V, et al.
J Chem Inf Model
. 2024 Jul;
64(15):6092-6104.
PMID: 39002142
Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis...
6.
Chen L, Roe D, Kochert M, Simmerling C, Alain Miranda-Quintana R
J Chem Theory Comput
. 2024 Jun;
20(13):5583-5597.
PMID: 38905589
One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as -means++...
7.
Cao X, Hummel M, Wang Y, Simmerling C, Coutsias E
J Chem Theory Comput
. 2024 May;
20(11):4456-4468.
PMID: 38780181
In this paper, we present differentiable solvent-accessible surface area (dSASA), an exact geometric method to calculate SASA analytically along with atomic derivatives on GPUs. The atoms in a molecule are...
8.
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, et al.
Biophys J
. 2024 May;
123(17):2902-2909.
PMID: 38751115
The precise prediction of major histocompatibility complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning...
9.
Casalino L, Dommer A, Gaieb Z, Barros E, Sztain T, Ahn S, et al.
Int J High Perform Comput Appl
. 2024 Apr;
35(5):432-451.
PMID: 38603008
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of...
10.
Chen L, Roe D, Kochert M, Simmerling C, Alain Miranda-Quintana R
bioRxiv
. 2024 Mar;
PMID: 38496504
One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as -means++...