4.3 Article

Potential of mean force and umbrella sampling simulation for the transport of 5-oxazolidinone in heterotetrameric sarcosine oxidase

Related references

Note: Only part of the references are listed.
Article Chemistry, Medicinal

Role of Molecular Dynamics and Related Methods in Drug Discovery

Marco De Vivo et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

Article Chemistry, Physical

A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A

Toni Giorgino et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Biochemistry & Molecular Biology

Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96

Tomotaka Moriguchi et al.

JOURNAL OF BIOCHEMISTRY (2010)

Article Chemistry, Physical

g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Jochen S. Hub et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Biochemistry & Molecular Biology

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff-Larsen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

Paul Labute

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Free energy calculations with non-equilibrium methods: applications of the Jarzynski relationship

Hui Xiong et al.

THEORETICAL CHEMISTRY ACCOUNTS (2006)

Article Biochemistry & Molecular Biology

Heterotetrameric sarcosine oxidase: Structure of a diflavin metalloenzyme at 1.85 A resolution

Zhi-wei Chen et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemical Research Methods

CysxHisy-Zn2+ interactions:: Possibilities and limitations of a simple pairwise force field

N Calimet et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Article Biochemistry & Molecular Biology

Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp U-96

K Ida et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2005)

Article Chemistry, Physical

Calculating potentials of mean force from steered molecular dynamics simulations

S Park et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)