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A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

artículo científico publicado en 2010

A Method for Conformational Sampling of Loops in Proteins Based on Adiabatic Decoupling and Temperature or Force Scaling ⬇️

artículo científico publicado el 26 de agosto de 2011

A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation

article

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.

artículo científico publicado en 2002

A comparison of methods to compute the potential of mean force

artículo científico publicado en 2007

A comparison of pathway-independent and pathway-dependent methods in the calculation of conformational free enthalpy differences

artículo científico publicado en 2015

A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability.

artículo científico publicado en 2010

A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase

artículo científico publicado en 2001

A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

artículo científico publicado en 2003

A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations

artículo científico publicado en 2001

A method to apply bond-angle constraints in molecular dynamics simulations

artículo científico publicado en 2020

A method to explore protein side chain conformational variability using experimental data

artículo científico publicado en 2009

A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents

artículo científico publicado en 2016

A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH.

artículo científico publicado en 2008

A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer

artículo científico publicado en 2005

A new force field for simulating phosphatidylcholine bilayers

artículo científico publicado en 2010

A photoinducible beta-hairpin.

artículo científico publicado en 2005

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

artículo científico publicado en 2014

A refined, efficient mean solvation force model that includes the interior volume contribution

artículo científico publicado en 2011

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations

article

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

article

Accounting for polarization in molecular simulation

Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations

scientific article published on 01 January 2020

Amine hydration: a united-atom force-field solution

artículo científico publicado en 2005

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

artículo científico publicado en 2011

An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixtures

article

An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations

artículo científico publicado en 2005

An effective force field for molecular dynamics simulations of dimethyl sulfone

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

An improved nucleic acid parameter set for the GROMOS force field

An improved simple polarisable water model for use in biomolecular simulation

article

An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation ⬇️

artículo científico publicado el 16 de junio de 2012

Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution?

artículo científico publicado en 2004

Assessing equilibration and convergence in biomolecular simulations

artículo científico publicado en 2002

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution

artículo científico publicado en 2012

Atomic models of de novo designed cc beta-Met amyloid-like fibrils

artículo científico publicado en 2007

Basic ingredients of free energy calculations: a review

artículo científico publicado en 2010

Biomolecular modeling: Goals, problems, perspectives

artículo científico publicado en 2006

Biomolecular simulation: historical picture and future perspectives.

artículo científico publicado en 2008

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation

artículo científico publicado en 2007

Biomolecular structure refinement using the GROMOS simulation software

artículo científico publicado en 2011

Calculating zeros: Non-equilibrium free energy calculations

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry

Calculation of binding free energies of inhibitors to plasmepsin II.

artículo científico publicado en 2011

Calculation of relative free energy via indirect pathways

Calculation of the Free Energy of Polarization: Quantifying the Effect of Explicitly Treating Electronic Polarization on the Transferability of Force-Field Parameters

artículo científico publicado en 2007

Calculation of the Redox Potential of the Protein Azurin and Some Mutants

scientific article published in 2005

Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9.

artículo científico publicado en 2012

Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum?

scientific article published on 01 November 2002

Carbopeptoid folding: effects of stereochemistry, chain length, and solvent

artículo científico publicado en 2004

Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data

artículo científico publicado en 2006

Challenge of representing entropy at different levels of resolution in molecular simulation

artículo científico publicado en 2014

Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations

artículo científico publicado en 2005

Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations

artículo científico publicado en 2015

Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

artículo científico publicado en 2004

Chemical library subset selection algorithms: a unified derivation using spatial statistics

artículo científico publicado en 2002

Circular dichroism spectra of β-peptides: sensitivity to molecular structure and effects of motional averaging

artículo científico publicado en 2003

Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol

artículo científico publicado en 2012

Combination of Enveloping Distribution Sampling (EDS) of a Soft-Core Reference-State Hamiltonian with One-Step Perturbation to Predict the Effect of Side Chain Substitution on the Relative Stability of Right- and Left-Helical Folds of β-Peptides

artículo científico publicado en 2012

Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen: The Effect of Explicitly Including Solvent Polarization

article

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

artículo científico publicado en 2006

Comparing geometric and kinetic cluster algorithms for molecular simulation data

artículo científico publicado en 2010

Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models

artículo científico publicado en 2007

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

artículo científico publicado en 2006

Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors

artículo científico publicado en 2011

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study

artículo científico publicado en 2004

Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.

artículo científico publicado en 2009

Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands

artículo científico publicado en 2007

Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations

artículo científico publicado en 2006

Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase

artículo científico publicado en 2008

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

artículo científico publicado en 2006

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding

artículo científico publicado en 2006

Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.

artículo científico publicado en 2007

Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data

scientific article published on 25 March 2019

Conformational and dynamical properties of disaccharides in water: a molecular dynamics study

artículo científico publicado en 2006

Conformational state‐specific free energy differences by one‐step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields ⬇️

artículo científico publicado el 3 de mayo de 2011

Correction to "Polarizable Model for DMSO and DMSO-Water Mixtures".

artículo científico publicado en 2016

Current computer modeling cannot explain why two highly similar sequences fold into different structures

artículo científico publicado en 2011

Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics

artículo científico publicado en 2010

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

artículo científico publicado en 2011

Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L

article

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

artículo científico publicado en 2016

Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.

artículo científico publicado en 2009

Development of a simple, self-consistent polarizable model for liquid water

article

Directed evolution of a model primordial enzyme provides insights into the development of the genetic code

artículo científico publicado en 2013

Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment

artículo científico publicado en 2008

Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures

artículo científico publicado en 2011

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

artículo científico publicado en 2004

Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide

artículo científico publicado en 2015

Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations

article

Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients

artículo científico publicado en 2013

Enhanced conformational sampling using enveloping distribution sampling

artículo científico publicado en 2013

Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling ⬇️

artículo científico publicado el 14 de septiembre de 2011

Enhancing the Configurational Sampling of Ions in Aqueous Solution Using Adiabatic Decoupling with Translational Temperature Scaling ⬇️

artículo científico publicado el 9 de marzo de 2011

Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation

artículo científico publicado en 2004

Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin

artículo científico publicado en 2002

Enveloping distribution sampling: a method to calculate free energy differences from a single simulation

scientific article published on 01 May 2007

Erratum: "Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system" [J. Chem. Phys. 137, 044120 (2012)]

scientific article published on 01 March 2017

Ester‐linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation – possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold ⬇️

artículo científico publicado el 9 de diciembre de 2011

Estimating entropies from molecular dynamics simulations

article

Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations

artículo científico publicado en 2008

Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups.

artículo científico publicado en 2009

Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water

artículo científico publicado en 2007

Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase.

artículo científico publicado en 2013

Exploring the Conserved Water Site and Hydration of a Coiled‐Coil Trimerisation Motif: A MD Simulation Study

artículo científico publicado en 2008

Exploring the Effect of Side-Chain Substitutions upon the Secondary Structure Preferences of β-Peptides ⬇️

artículo científico publicado el 14 de octubre de 2011

Exploring the properties of small molecule protein binding via molecular simulations: the TRSH–p53 core domain complex ⬇️

artículo científico publicado el 1 de noviembre de 2012

Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

artículo científico publicado en 2010

Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations

artículo científico publicado en 2015

Folding and unfolding of two mixed alpha/beta peptides

artículo científico publicado en 2009

Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations

scholarly article by Xavier Daura published in February 1999

Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents

artículo científico publicado en 2006

Force-field dependence of the conformational properties of α,ω-dimethoxypolyethylene glycol

article published in 2009

Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions

scientific article published in 1996

Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water

artículo científico publicado en 2013

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

artículo científico publicado en 2004

Free energies of ligand binding for structurally diverse compounds

artículo científico publicado en 2005

Free energy barrier estimation of unfolding the ?-helical surfactant-associated polypeptide C

scholarly article by Ronen Zangi published in January 2001

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities

artículo científico publicado en 2011

Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations

artículo científico publicado en 2007

Free enthalpies of replacing water molecules in protein binding pockets

artículo científico publicado en 2012

GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.

artículo científico publicado en 2015

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

artículo científico publicado en 2011

Helical content of a β(3)-octapeptide in methanol: molecular dynamics simulations explain a seeming discrepancy between conclusions derived from CD and NMR data

artículo científico publicado en 2011

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

artículo científico publicado en 2012

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

artículo científico publicado en 2009

Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study

artículo científico publicado en 2012

Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide.

artículo científico publicado en 2009

Influence of variation of a side chain on the folding equilibrium of a β‐peptide: Limitations of one‐step perturbation ⬇️

artículo científico publicado el 24 de mayo de 2013

Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages ⬇️

artículo científico publicado el 27 de junio de 2012

Interpretation of Seemingly Contradictory Data: Low NMR S2 Order Parameters Observed in Helices and High NMR S2 Order Parameters in Disordered Loops of the Protein hGH at Low pH.

artículo científico publicado en 2017

Interpreting NMR data for beta-peptides using molecular dynamics simulations

artículo científico publicado en 2005

Interpreting experimental data by using molecular simulation instead of model building

artículo científico publicado en 2009

Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers

artículo científico publicado en 2013

Investigation of Stability and Disulfide Bond Shuffling of Lipid Transfer Proteins by Molecular Dynamics Simulation

article

Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion

artículo científico publicado en 2016

Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA.

artículo científico publicado en 2007

Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle

artículo científico publicado en 2010

Methane clustering in explicit water: effect of urea on hydrophobic interactions

artículo científico publicado en 2005

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

artículo científico publicado en 2010

Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system

article

Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation

artículo científico publicado en 2004

Molecular dynamics simulation of the last step of a catalytic cycle: Product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis ⬇️

artículo científico publicado el 1 de noviembre de 2012

Molecular dynamics simulation of thionated hen egg white lysozyme ⬇️

artículo científico publicado el 25 de junio de 2012

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

artículo científico publicado en 2005

Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: comparisons of the wild-type protein, a b-type variant, and the apo state

artículo científico publicado en 2006

Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells

scientific article published on 01 August 2002

Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data.

artículo científico publicado en 2013

Molecular dynamics simulations of liquid methanol and methanol–water mixtures with polarizable models

article

Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time

artículo científico publicado en 2005

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

artículo científico publicado en 2002

Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra?

artículo científico publicado en 2003

Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection

Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics.

artículo científico publicado en 2007

Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA

artículo científico publicado en 2010

Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase

article

Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins

article

Molecular simulation as an aid to experimentalists.

artículo científico publicado en 2008

Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

article

Multi-resolution simulation of biomolecular systems: a review of methodological issues

artículo científico publicado en 2013

Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems

artículo científico publicado en 2006

Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.

artículo científico publicado en 2013

Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions

artículo científico publicado en 2008

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

artículo científico publicado en 2011

New functionalities in the GROMOS biomolecular simulation software

artículo científico publicado en 2011

Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer

artículo científico publicado en 2005

On developing coarse-grained models for biomolecular simulation: a review

artículo científico

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

artículo científico publicado en 2008

On the Calculation of Atomic Forces in Classical Simulation Using the Charge-on-Spring Method To Explicitly Treat Electronic Polarization

article

On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase

article

On the Conformational Properties of Amylose and Cellulose Oligomers in Solution

article published in 2009

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

artículo científico publicado en 2020

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters

scientific article published on 01 January 2014

On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices

scientific article published on 11 November 2011

On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme

artículo científico publicado en 2020

On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water

artículo científico publicado en 2013

On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm

artículo científico publicado en 2007

On the calculation of ³Jαβ-coupling constants for side chains in proteins.

artículo científico publicado en 2012

On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment

artículo científico publicado en 2012

On the direct calculation of the free energy of quantization for molecular systems in the condensed phase

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

artículo científico publicado en 2011

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study

artículo científico publicado en 2005

On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations

artículo científico publicado en 2015

On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters

artículo científico publicado en 2014

On the use of time-averaging restraints when deriving biomolecular structure from [Formula: see text]-coupling values obtained from NMR experiments

artículo científico publicado en 2016

On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.

artículo científico publicado en 2009

On using oscillating time-dependent restraints in MD simulation

artículo científico publicado en 2006

Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach

artículo científico publicado en 1998

Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulation

artículo científico publicado en 2006

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

Peptide Folding: When Simulation Meets Experiment

scholarly article by Xavier Daura et al published 15 January 1999 in Angewandte Chemie

Peptide folding simulations: no solvent required?

Peptides of Aminoxy Acids: A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions

article

Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane

artículo científico publicado en 2015

Polarizable model for DMSO and DMSO-water mixtures

artículo científico publicado en 2014

Practical Aspects of Free-Energy Calculations: A Review

artículo científico

Prediction of folding equilibria of differently substituted peptides using one-step perturbation

artículo científico publicado en 2010

Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces

scientific article published on 02 November 2011

Principles of carbopeptoid folding: a molecular dynamics simulation study

artículo científico publicado en 2005

Protein under pressure: molecular dynamics simulation of the arc repressor.

artículo científico publicado en 2006

Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation

artículo científico publicado en 2014

QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians

artículo científico publicado en 2007

Rapid Sampling of Folding Equilibria of β-Peptides in Methanol Using a Supramolecular Solvent Model

artículo científico publicado en 2014

Recent advances in computational actinoid chemistry.

artículo científico publicado en 2012

Refinement of the application of the GROMOS 54A7 force field to β-peptides

artículo científico publicado en 2013

Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds

artículo científico publicado en 2013

Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol

artículo científico publicado en 2012

Reply

scholarly article by Wilfred F. Van Gunsteren et al published 17 December 2001 in Angewandte Chemie International Edition

Sampling of rare events using hidden restraints

scientific article published on 01 April 2006

Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS).

artículo científico publicado en 2009

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation

artículo científico publicado en 2002

Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety

Simulation of Folding Equilibria

Simulation of an all-beta 3-icosapeptide containing the 20 proteinogenic side chains: effect of temperature, pH, counterions, solvent, and force field on helix stability

artículo científico publicado en 2006

Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria

scientific article published on 01 March 2007

Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.

artículo científico publicado en 2002

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character

artículo científico publicado en 2003

Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations

artículo científico publicado en 2012

Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water

artículo científico publicado en 2012

Structure Optimization Combining Soft-Core Interaction Functions, the Diffusion Equation Method, and Molecular Dynamics

article

Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics Simulations

article

Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment

scientific article published on 27 March 2008

Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling.

artículo científico publicado en 2010

Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data ⬇️

artículo científico publicado el 14 de marzo de 2013

Studying the Stability of a Helical β-Heptapeptide by Molecular Dynamics Simulations

article

Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase

artículo científico publicado en 2015

Temperature Dependence of the Dielectric Permittivity of Acetic Acid, Propionic Acid and Their Methyl Esters: A Molecular Dynamics Simulation Study

article

Terminal-group effects on the folding behavior of selected beta-peptides

scientific article published on 01 April 2006

The GROMOS Biomolecular Simulation Program Package

The GROMOS software for biomolecular simulation: GROMOS05.

artículo científico publicado en 2005

The GROMOS96 benchmarks for molecular simulation

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The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged

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