4.6 Article

Accounting for the instantaneous disorder in the enzyme-substrate Michaelis complex to calculate the Gibbs free energy barrier of an enzyme reaction

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5

Beatriz von der Esch et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Multidisciplinary

Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations

Jernej Stare

RSC ADVANCES (2017)

Article Chemistry, Physical

How Can Linoleic Acid Be the Preferential Substrate of the Enzyme 15-Lipoxygenase-1? A QM/MM Approach

Jordi Soler et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2016)

Article Chemistry, Medicinal

MCPB.py: A Python Based Metal Center Parameter Builder

Pengfei Li et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Chemistry, Physical

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Arieh Warshel et al.

JOURNAL OF CHEMICAL PHYSICS (2016)

Article Multidisciplinary Sciences

Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins

Susan Adel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Review Biochemistry & Molecular Biology

The structural basis for specificity in lipoxygenase catalysis

Marcia E. Newcomer et al.

PROTEIN SCIENCE (2015)

Article Chemistry, Physical

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

Antonio J. M. Ribeiro et al.

ACS CATALYSIS (2015)

Article Chemistry, Physical

Averaging Techniques for Reaction Barriers in QM/MM Simulations

April M. Cooper et al.

CHEMPHYSCHEM (2014)

Article Biochemistry & Molecular Biology

Enzymatic Rate Enhancements: A Review and Perspective

John P. Richard

BIOCHEMISTRY (2013)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Romelia Salomon-Ferrer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Conformational Compression and Barrier Height Heterogeneity in the N-Acetylglutamate Kinase

Melchor Sanchez-Martinez et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Multidisciplinary

A Mechanistic Hypothesis for the Aspirin-Induced Switch in Lipid Mediator Production by Cyclooxygenase-2

Paolo Tosco

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Chemistry, Multidisciplinary

Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9

Richard Lonsdale et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Review Biotechnology & Applied Microbiology

Lipoxygenases: Potential starting biocatalysts for the synthesis of signaling compounds

Young-Chul Joo et al.

BIOTECHNOLOGY ADVANCES (2012)

Article Chemistry, Physical

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Goetz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Multidisciplinary

The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations

Antonio J. M. Ribeiro et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemistry & Molecular Biology

H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

Ramu Anandakrishnan et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Chemistry, Multidisciplinary

Lipoxygenase and Leukotriene Pathways: Biochemistry, Biology, and Roles in Disease

Jesper Z. Haeggstrom et al.

CHEMICAL REVIEWS (2011)

Review Biochemistry & Molecular Biology

Functional and pathological roles of the 12-and 15-lipoxygenases

Anca D. Dobrian et al.

PROGRESS IN LIPID RESEARCH (2011)

Article Chemistry, Physical

Compound I Reactivity Defines Alkene Oxidation Selectivity in Cytochrome P450cam

Richard Lonsdale et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Biochemistry & Molecular Biology

Free-energy landscape of enzyme catalysis

Stephen J. Benkovic et al.

BIOCHEMISTRY (2008)

Article Multidisciplinary Sciences

On the relationship between folding and chemical landscapes in enzyme catalysis

Malte Roca et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data

Jongkeun Choi et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Review Chemistry, Multidisciplinary

GLYCAM06: A generalizable Biomolecular force field. Carbohydrates

Karl N. Kirschner et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

Silvia Ferrer et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Review Chemistry, Multidisciplinary

Single molecule studies of enzyme mechanisms

R. Derike Smiley et al.

CHEMICAL REVIEWS (2006)

Review Chemistry, Multidisciplinary

Fluctuating enzymes: Lessons from single-molecule studies

W Min et al.

ACCOUNTS OF CHEMICAL RESEARCH (2005)

Article Chemistry, Physical

Single-molecule Michaelis-Menten equations

SC Kou et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Multidisciplinary

Conformational substates modulate hydride transfer in dihydrofolate reductase

IF Thorpe et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Biochemistry & Molecular Biology

H++:: a server for estimating pKas and adding missing hydrogens to macromolecules

JC Gordon et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Multidisciplinary Sciences

Protein conformational dynamics probed by single-molecule electron transfer

H Yang et al.

SCIENCE (2003)

Article Chemistry, Physical

Generalized transition state theory in terms of the potential of mean force

GK Schenter et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

Review Chemistry, Physical

QUASI:: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

P Sherwood et al.

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (2003)

Review Chemistry, Multidisciplinary

The depth of chemical time and the power of enzymes as catalysts

R Wolfenden et al.

ACCOUNTS OF CHEMICAL RESEARCH (2001)

Article Chemistry, Physical

Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates

SR Billeter et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2000)