Sameer Varma
Overview
Explore the profile of Sameer Varma including associated specialties, affiliations and a list of published articles.
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Articles
46
Citations
638
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Recent Articles
1.
Guergues J, Wohlfahrt J, Koomen J, Krieger J, Varma S, Stevens Jr S
Proteomics
. 2024 Sep;
25(3):e2400129.
PMID: 39235396
Targeted proteomics, which includes parallel reaction monitoring (PRM), is typically utilized for more precise detection and quantitation of key proteins and/or pathways derived from complex discovery proteomics datasets. Initial discovery-based...
2.
Higbee P, Dayhoff 2nd G, Anbanandam A, Varma S, Daughdrill G
J Mol Biol
. 2024 May;
436(13):168626.
PMID: 38810774
The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16-29, 17-35, and 1-73. All the peptides had large, negative heat capacity...
3.
Delgado J, Nagy P, Varma S
J Chem Inf Model
. 2023 Dec;
64(2):378-392.
PMID: 38051630
Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also...
4.
Cueny R, Varma S, Schmidt K, Keck J
PLoS One
. 2023 Jun;
18(6):e0281524.
PMID: 37267408
Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome...
5.
Cueny R, Varma S, Schmidt K, Keck J
bioRxiv
. 2023 Feb;
PMID: 36747637
Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human cause Bloom syndrome (BS),...
6.
Delgado J, Wineman-Fisher V, Pandit S, Varma S
J Chem Inf Model
. 2022 Sep;
62(19):4713-4726.
PMID: 36173398
The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to...
7.
Saunders M, Wineman-Fisher V, Jakobsson E, Varma S, Pandit S
Langmuir
. 2022 Feb;
38(9):2840-2851.
PMID: 35192365
Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using...
8.
Varma S, Orgel J, Schieber J
Int J Mol Sci
. 2021 Aug;
22(16).
PMID: 34445791
Collagen is heavily hydroxylated. Experiments show that proline hydroxylation is important to triple helix (monomer) stability, fibril assembly, and interaction of fibrils with other molecules. Nevertheless, experiments also show that...
9.
Varma S, Dey S, Palanisamy D
Curr Pharm Biotechnol
. 2021 Jul;
23(5):679-706.
PMID: 34264182
Background: Efficient and controlled internalization of NPs into the cells depends on their physicochemical properties and dynamics of the plasma membrane. NPs-cell interaction is a complex process that decides the...
10.
Rahman S, Wineman-Fisher V, Nagy P, Al-Hamdani Y, Tkatchenko A, Varma S
Chemistry
. 2021 May;
27(42):11005-11014.
PMID: 33999467
Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain...