Volodymyr Babin

Works (12)

Updated: July 5th, 2023 15:56

2015 article

The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

By: M. Moradi *, V. Babin n, C. Roland n & C. Sagui n

TL;DR: The workings of the ABMD method are reviewed with an emphasis on recent software additions, along with a short summary of a selected ABMD application based on the B-to-Z DNA transition. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2013 journal article

Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

PLOS COMPUTATIONAL BIOLOGY, 9(8).

By: V. Babin n, D. Wang n, R. Rose  n & C. Sagui n

TL;DR: Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity and propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2010 journal article

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

JOURNAL OF CHEMICAL PHYSICS, 133(12).

By: M. Moradi n, V. Babin n, C. Roland n & C. Sagui n

MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Phase Transition; Protein Conformation; Thermodynamics
TL;DR: This work characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment and quantitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. (via Semantic Scholar)
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2010 journal article

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

JOURNAL OF CHEMICAL PHYSICS, 132(10).

By: V. Babin n & C. Sagui n

author keywords: free energy; molecular dynamics method; organic compounds; simulation
MeSH headings : Algorithms; Carbohydrate Sequence; Computer Simulation; Glucuronic Acid / chemistry; Iduronic Acid / chemistry; Molecular Conformation; Molecular Sequence Data; Thermodynamics; Water / chemistry
TL;DR: A simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent is presented and applied to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic Acid in water. (via Semantic Scholar)
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2010 journal article

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

International Journal of Quantum Chemistry, 110(15), 2865–2879.

By: M. Moradi, J. Lee, V. Babin, C. Roland & C. Sagui

Source: NC State University Libraries
Added: August 6, 2018

2009 article

Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, December). INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 109, pp. 3666–3678.

By: V. Babin n, V. Karpusenka n, M. Moradi n, C. Roland n & C. Sagui n

author keywords: free energy; nonequilibrium; simulation
TL;DR: The workings of the ABMD method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short -turn peptide. (via Semantic Scholar)
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2009 journal article

Conformations and free energy landscapes of polyproline peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(49), 20746–20751.

By: M. Moradi n, V. Babin n, C. Roland n, T. Darden & C. Sagui n

author keywords: cis-trans isomerization; left-handed helix; molecular dynamics; PPI; PPII
MeSH headings : Peptides / chemistry; Protein Conformation; Thermodynamics
TL;DR: Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the exist of stable heterogeneous subpopulations in PPII polyproline. (via Semantic Scholar)
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2008 journal article

Adaptively biased molecular dynamics for free energy calculations

Journal of Chemical Physics, 128(13).

By: V. Babin n, C. Roland n & C. Sagui n

TL;DR: The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment. (via Semantic Scholar)
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Source: NC State University Libraries
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2006 journal article

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 110(5), 2325–2331.

By: J. Lee n, E. Asciutto n, V. Babin n, C. Sagui n, T. Darden n & C. Roland n

MeSH headings : Computational Biology; Computer Simulation; Formates / chemistry; Hydrogen / chemistry; Models, Molecular; Oxygen / chemistry; Protons; Solvents / chemistry; Thermodynamics; Time Factors
TL;DR: The microscopics of deprotonation and reprotonation of formic acid reveal the key role played by nearby water molecules in catalyzing the reactions, and reveal barriers similar to that obtained with the constrained free-energy calculation. (via Semantic Scholar)
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2006 journal article

Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

JOURNAL OF PHYSICAL CHEMISTRY B, 110(23), 11571–11581.

By: V. Babin n, J. Baucom n, T. Darden n & C. Sagui n

MeSH headings : Base Sequence; Crystallography; DNA / chemistry; Nucleic Acid Conformation
TL;DR: This is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD. (via Semantic Scholar)
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Source: Web Of Science
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2006 journal article

Molecular dynamics simulations of polarizable DNA in crystal environment

International Journal of Quantum Chemistry, 106(15), 3260–3269.

By: V. Babin n, J. Baucom n, T. Darden* & C. Sagui n

author keywords: DNA; electrostatics; polarizable; crystal
TL;DR: By imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. (via Semantic Scholar)
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Sources: Web Of Science, Crossref
Added: August 6, 2018

2006 journal article

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

JOURNAL OF CHEMICAL PHYSICS, 125(20).

By: V. Babin n, C. Roland n, T. Darden* & C. Sagui n

MeSH headings : Algorithms; Computer Simulation; Energy Transfer; Kinetics; Models, Chemical; Models, Molecular; Peptides / chemistry; Protein Conformation
TL;DR: It is shown that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques, and is to be distributed in the next scheduled release of the code. (via Semantic Scholar)
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Source: Web Of Science
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