Biomolecular free energy profiles by a shooting/umbrella sampling protocol, “BOLAS”
|
journal
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August 2004 |
Nitrogen-15 NMR spectroscopy of hydrogen-bonding interactions in the active site of serine proteases: evidence for a moving histidine mechanism
|
journal
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November 1986 |
Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate
|
journal
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January 2011 |
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
|
journal
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February 1977 |
How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations
|
journal
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January 2004 |
Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism
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journal
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December 2008 |
Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights
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journal
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June 2003 |
Scalable molecular dynamics with NAMD
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journal
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January 2005 |
The Amber biomolecular simulation programs
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journal
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January 2005 |
Using the histogram test to quantify reaction coordinate error
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journal
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December 2006 |
Theoretical Studies on the Deacylation Step of Serine Protease Catalysis in the Gas Phase, in Solution, and in Elastase
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journal
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November 2004 |
What can feruloyl esterases do for us?
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journal
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December 2009 |
Obtaining reaction coordinates by likelihood maximization
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journal
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August 2006 |
Multiple Conformations of Catalytic Serine and Histidine in Acetylxylan Esterase at 0.90 Å
|
journal
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April 2001 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
|
journal
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March 1977 |
The pharmacological landscape and therapeutic potential of serine hydrolases
|
journal
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January 2012 |
Biomass recalcitrance: a multi-scale, multi-factor, and conversion-specific property: Fig. 1.
|
journal
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June 2015 |
Catalysis by Glomerella cingulata Cutinase Requires Conformational Cycling between the Active and Inactive States of Its Catalytic Triad
|
journal
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January 2009 |
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
|
journal
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October 2002 |
The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies
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journal
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December 2013 |
Comparison of simple potential functions for simulating liquid water
|
journal
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July 1983 |
Feruloyl Esterase: A Key Enzyme in Biomass Degradation
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journal
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January 2006 |
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
|
journal
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September 1998 |
Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates
|
journal
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April 2006 |
Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases
|
journal
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January 2016 |
Structural diversity of carbohydrate esterases
|
journal
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January 2017 |
Enzymes as Green Catalysts for Precision Macromolecular Synthesis
|
journal
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January 2016 |
CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software
|
journal
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December 2009 |
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
|
journal
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November 2008 |
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
|
journal
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January 2009 |
Low-barrier hydrogen bonds and enzymic catalysis
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journal
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June 1994 |
Solvent reaction coordinate for an S N 2 reaction
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journal
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July 2020 |
Structure of a feruloyl esterase from Aspergillus niger
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journal
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April 2004 |
Constant pressure molecular dynamics simulation: The Langevin piston method
|
journal
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September 1995 |
Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The Reaction Free Energy Profiles of the Acylation Process
|
journal
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October 2003 |
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
|
journal
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October 1983 |
Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals
|
journal
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July 2011 |
Hydrogen Tunneling in Enzymes and Biomimetic Models
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journal
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December 2013 |
Serine Protease Mechanism and Specificity
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journal
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December 2002 |
A bacterium that degrades and assimilates poly(ethylene terephthalate)
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journal
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March 2016 |
The faeA genes from Aspergillus niger and Aspergillus tubingensis encode ferulic acid esterases involved in degradation of complex cell wall polysaccharides.
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journal
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January 1997 |
Unusual 1H NMR chemical shifts support (His) Cepsilon 1---H{middle dot}{middle dot}{middle dot}O==C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis
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journal
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September 2000 |
From transition paths to transition states and rate coefficients
|
journal
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January 2004 |
Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation
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journal
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January 2014 |
Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications
|
journal
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October 2016 |
Serine Proteases: Structure and Mechanism of Catalysis
|
journal
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June 1977 |
Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes
|
journal
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March 2010 |
Looking at Self-Consistent-Charge Density Functional Tight Binding from a Semiempirical Perspective †
|
journal
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July 2007 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
|
journal
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June 1993 |
Fundamental Reaction Pathway and Free Energy Profile for Butyrylcholinesterase-Catalyzed Hydrolysis of Heroin
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journal
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August 2013 |
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
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journal
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July 2005 |
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package †
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journal
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July 2007 |
Molecular dynamics with coupling to an external bath
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journal
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October 1984 |
Ab Initio QM/MM Dynamics Simulation of the Tetrahedral Intermediate of Serine Proteases: Insights into the Active Site Hydrogen-Bonding Network
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journal
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December 2002 |
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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journal
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August 2012 |
The Crystal Structure of Feruloyl Esterase A from Aspergillus niger Suggests Evolutive Functional Convergence in Feruloyl Esterase Family
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journal
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April 2004 |
Mechanisms and Free Energies of Enzymatic Reactions
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journal
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August 2006 |
Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
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journal
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December 2010 |
The catalytic triad of serine peptidases
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journal
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July 2005 |
Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger
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journal
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September 2005 |
The Dynamical Nature of Enzymatic Catalysis
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journal
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December 2014 |
How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes
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journal
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September 2015 |
Recent developments in methods for identifying reaction coordinates
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journal
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April 2014 |
The implementation of a fast and accurate QM/MM potential method in Amber
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journal
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January 2008 |
Structural insight into catalytic mechanism of PET hydrolase
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journal
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December 2017 |
Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review
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journal
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July 2015 |
Extensions to the likelihood maximization approach for finding reaction coordinates
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journal
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July 2007 |
Reaction Coordinates and Mechanistic Hypothesis Tests
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journal
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May 2016 |
Structural Basis for the Substrate Specificity of the Feruloyl Esterase Domain of the Cellulosomal Xylanase Z from Clostridium thermocellum †
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journal
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October 2001 |
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
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journal
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February 2006 |
The Structure of the Feruloyl Esterase Module of Xylanase 10B from Clostridium thermocellum Provides Insights into Substrate Recognition
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journal
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December 2001 |
Characterization and engineering of a plastic-degrading aromatic polyesterase
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journal
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April 2018 |
Density functional tight binding: application to organic and biological molecules: Density functional tight binding
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journal
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June 2013 |