Armen RS - Search Results

1

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Armen RS, Chen J, Brooks CL 3rd. Armen RS, et al. J Chem Theory Comput. 2009 Oct 13;5(10):2909-2923. doi: 10.1021/ct900262t. J Chem Theory Comput. 2009. PMID: 20160879 Free PMC article.

2

Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes.

Armen RS, Schiller SM, Brooks CL 3rd. Armen RS, et al. Proteins. 2010 Jun;78(8):1926-38. doi: 10.1002/prot.22706. Proteins. 2010. PMID: 20310065 Free PMC article.

3

The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners.

May ER, Armen RS, Mannan AM, Brooks CL 3rd. May ER, et al. Among authors: armen rs. Proteins. 2010 Aug 1;78(10):2251-64. doi: 10.1002/prot.22738. Proteins. 2010. PMID: 20544962 Free PMC article.

4

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

Rahaman O, Estrada TP, Doren DJ, Taufer M, Brooks CL 3rd, Armen RS. Rahaman O, et al. Among authors: armen rs. J Chem Inf Model. 2011 Sep 26;51(9):2047-65. doi: 10.1021/ci1003009. Epub 2011 Jun 6. J Chem Inf Model. 2011. PMID: 21644546 Free PMC article.

5

Computational multiscale modeling in protein--ligand docking.

Taufer M, Armen R, Chen J, Teller P, Brooks C. Taufer M, et al. IEEE Eng Med Biol Mag. 2009 Mar-Apr;28(2):58-69. doi: 10.1109/MEMB.2009.931789. IEEE Eng Med Biol Mag. 2009. PMID: 19349252

6

A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

Estrada T, Zhang B, Cicotti P, Armen RS, Taufer M. Estrada T, et al. Among authors: armen rs. Comput Biol Med. 2012 Jul;42(7):758-71. doi: 10.1016/j.compbiomed.2012.05.001. Epub 2012 Jun 2. Comput Biol Med. 2012. PMID: 22658682

7

Identification of distant drug off-targets by direct superposition of binding pocket surfaces.

Schumann M, Armen RS. Schumann M, et al. Among authors: armen rs. PLoS One. 2013 Dec 31;8(12):e83533. doi: 10.1371/journal.pone.0083533. eCollection 2013. PLoS One. 2013. PMID: 24391782 Free PMC article.

8

Modeling the Structure-Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein.

Freidel MR, Armen RS. Freidel MR, et al. Among authors: armen rs. J Chem Inf Model. 2021 Dec 27;61(12):5906-5922. doi: 10.1021/acs.jcim.1c01061. Epub 2021 Dec 13. J Chem Inf Model. 2021. PMID: 34898207 Free PMC article.

9

Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase.

Freidel MR, Armen RS. Freidel MR, et al. Among authors: armen rs. PLoS One. 2021 Feb 17;16(2):e0246181. doi: 10.1371/journal.pone.0246181. eCollection 2021. PLoS One. 2021. PMID: 33596235 Free PMC article.

10

Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

Schumann M, Armen RS. Schumann M, et al. Among authors: armen rs. J Comput Chem. 2013 May 30;34(14):1258-69. doi: 10.1002/jcc.23251. Epub 2013 Feb 19. J Comput Chem. 2013. PMID: 23420703

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