List of works - Angel E. García

A statistical mechanical description of biomolecular hydration

scientific article published on January 1996

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering

scientific article

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

scientific article

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies

scientific article

An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface

scientific article published on May 2009

Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD

scientific article published on 27 June 2020

Atomic simulations of protein folding, using the replica exchange algorithm.

scientific article published in January 2004

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms ⬇️

scientific article published on November 5, 2010

Atomic-level description of amyloid beta-dimer formation

scientific article

Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach

scientific article published on 25 June 2013

Backbone and side-chain contributions in protein denaturation by urea

scientific article

Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C

scientific article published on 10 January 2013

Boundary integral methods for the Poisson equation of continuum dielectric solvation models

Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

scientific article

Cavities determine the pressure unfolding of proteins

scientific article

Cell penetrating peptides: how do they do it?

scientific article published on December 2007

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

scientific article published on 12 November 2015

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

scientific article published on 02 February 2022

Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape.

scientific article

Computing the stability diagram of the Trp-cage miniprotein

scholarly article

Conformational Diffusion and Helix Formation Kinetics

scientific article published in Physical Review Letters

Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain

scientific article

Correction of apparent finite size effects in the area per lipid of lipid membranes simulations

scientific article published in December 2006

Cosolvent effects on protein stability

scientific article published on 04 January 2013

Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study

scientific article

Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy.

scientific article

Effects of truncating van der Waals interactions in lipid bilayer simulations

scientific article

Efficient Schmidt number scaling in dissipative particle dynamics

scientific article

Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules

Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with Urea.

scientific article published on 9 February 2017

Equilibrium study of protein denaturation by urea

scientific article published in February 2010

Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin

scientific article published on 29 January 2014

Experimental Test of the Thermodynamic Model of Protein Cooperativity Using Temperature-Induced Unfolding of a Ubq−UIM Fusion Protein ⬇️

scientific article published on September 13, 2010

Exploring the energy landscape of a beta hairpin in explicit solvent

scientific article published on 01 February 2001

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A ⬇️

scientific article published on November 17, 2003

Folding a protein in the computer: reality or hope?

scientific article

Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein

scientific article published on 03 January 2014

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer

scientific article published on 01 June 2005

Folding of a highly conserved diverging turn motif from the SH3 domain

scientific article

Folding time predictions from all-atom replica exchange simulations

scientific article published on 17 July 2007

Free Energy of Ionic Hydration

Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation

scientific article published on January 2013

Free-energy landscape of a hyperstable RNA tetraloop

scientific article published on 27 May 2016

Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules

scientific article

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations

scientific article

Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures

scientific article published in June 2005

High pressure NMR reveals conformational perturbations by disease-causing mutations in amyloid β-peptide.

scientific article published on 19 April 2018

High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape

scientific article published on December 2016

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

scientific article

How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes

scientific article published on 21 May 2020

Hydration free energy of water

Hydration of an α‐Helical peptide: comparison of theory and molecular dynamics simulation

article

Impact of hydrodynamics on effective interactions in suspensions of active and passive matter.

scientific article

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

scientific article published on 15 August 2011

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

scientific article published on 01 February 2003

Ion sizes and finite-size corrections for ionic-solvation free energies

Local structure formation in simulations of two small proteins

scientific article published on 11 October 2006

MHC-peptide binding is assisted by bound water molecules

scientific article published in April 2004

Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations

scientific article

Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations.

scientific article

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B

article

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

scientific article published on June 2010

Mirror images as naturally competing conformations in protein folding.

scientific article

Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics

Molecular Theories and Simulation of Ions and Polar Molecules in Water

Molecular dynamics simulations of protein folding.

scientific article published in January 2008

Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes

scientific article

Molecular dynamics study of water penetration in staphylococcal nuclease.

scientific article

Molecular mechanism for the preferential exclusion of TMAO from protein surfaces

scientific article published on October 2012

Multi-basin dynamics of a protein in a crystal environment

article

Multisite ion model in concentrated solutions of divalent cations (MgCl2 and CaCl2): osmotic pressure calculations

scientific article

Multistate Gaussian Model for Electrostatic Solvation Free Energies

article

NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage.

scientific article published on 20 January 2017

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements

scholarly article

Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering.

scientific article

Peptide Bond Isomerization in High-Temperature Simulations.

scientific article published on 15 March 2016

Peptide folding simulations ⬇️

scientific article published on April 1, 2003

Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water.

scientific article

Please, get in my way so that I can be more efficient!

scientific article

Potential biophysical application of the Los Alamos infrared free electron laser: DNA spectroscopy

Preferential Interactions of Charged and Neutral Cosolutes with a Model RNA Hairpin

Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction

scientific article published on 14 March 2020

Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics

scientific article published on 11 July 2008

Protein conformational space populated in solution probed with aromatic residual dipolar (13) C-(1) H couplings

scientific article published on 12 March 2013

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

scientific article

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

scientific article

Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations

scientific article published on 25 July 2013

Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations

scientific article

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

scientific article

Reply to Comment on “Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules”

Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study

scientific article published on 02 December 2004

Role of Backbone Hydration and Salt-Bridge Formation in Stability of α-Helix in Solution ⬇️

scientific article published on November 1, 2003

Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins

scientific article

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent ⬇️

scientific article published on November 14, 2003

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

scientific article published on 23 December 2007

Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement.

scientific article

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

scientific article published on June 2011

Simulations of the pressure and temperature unfolding of an alpha-helical peptide.

scientific article

Size and sequence and the volume change of protein folding

scientific article

Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations.

scientific article

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

scientific article published in February 2002

Structure-based design of a heptavalent anthrax toxin inhibitor.

scientific article published on 8 February 2011

Studying pressure denaturation of a protein by molecular dynamics simulations

scientific article published in May 2010

The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study

scientific article

The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling

scientific article published on 22 January 2020

The essential role of stacking adenines in a two-base-pair RNA kissing complex

scientific article published on 8 April 2013

The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations

scientific article published on 23 February 2010

The solvent-dependent shift of the amide I band of a fully solvated peptide as a local probe for the solvent composition in the peptide/solvent interface.

scientific article published in December 2008

Tranilast binds to aβ monomers and promotes aβ fibrillation

scientific article published on 31 May 2013

V67L Mutation Fills an Internal Cavity To Stabilize RecA Mtu Intein

scientific article published on 10 May 2017

Water Determines the Structure and Dynamics of Proteins

scientific article

Water penetration in the low and high pressure native states of ubiquitin

scientific article

List of works by Angel E. García

A statistical mechanical description of biomolecular hydration

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies

An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface

Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD

Atomic simulations of protein folding, using the replica exchange algorithm.

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms ⬇️

Atomic-level description of amyloid beta-dimer formation

Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach

Backbone and side-chain contributions in protein denaturation by urea

Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C

Boundary integral methods for the Poisson equation of continuum dielectric solvation models

Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

Cavities determine the pressure unfolding of proteins

Cell penetrating peptides: how do they do it?

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape.

Computing the stability diagram of the Trp-cage miniprotein

Conformational Diffusion and Helix Formation Kinetics

Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain

Correction of apparent finite size effects in the area per lipid of lipid membranes simulations

Cosolvent effects on protein stability

Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study

Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy.

Effects of truncating van der Waals interactions in lipid bilayer simulations

Efficient Schmidt number scaling in dissipative particle dynamics

Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules

Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with Urea.

Equilibrium study of protein denaturation by urea

Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin

Experimental Test of the Thermodynamic Model of Protein Cooperativity Using Temperature-Induced Unfolding of a Ubq−UIM Fusion Protein ⬇️

Exploring the energy landscape of a beta hairpin in explicit solvent

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A ⬇️

Folding a protein in the computer: reality or hope?

Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer

Folding of a highly conserved diverging turn motif from the SH3 domain

Folding time predictions from all-atom replica exchange simulations

Free Energy of Ionic Hydration

Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation

Free-energy landscape of a hyperstable RNA tetraloop

Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations

Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures

High pressure NMR reveals conformational perturbations by disease-causing mutations in amyloid β-peptide.

High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes

Hydration free energy of water

Hydration of an α‐Helical peptide: comparison of theory and molecular dynamics simulation

Impact of hydrodynamics on effective interactions in suspensions of active and passive matter.

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

Ion sizes and finite-size corrections for ionic-solvation free energies

Local structure formation in simulations of two small proteins

MHC-peptide binding is assisted by bound water molecules

Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations

Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations.

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

Mirror images as naturally competing conformations in protein folding.

Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics

Molecular Theories and Simulation of Ions and Polar Molecules in Water

Molecular dynamics simulations of protein folding.

Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes

Molecular dynamics study of water penetration in staphylococcal nuclease.

Molecular mechanism for the preferential exclusion of TMAO from protein surfaces

Multi-basin dynamics of a protein in a crystal environment

Multisite ion model in concentrated solutions of divalent cations (MgCl2 and CaCl2): osmotic pressure calculations

Multistate Gaussian Model for Electrostatic Solvation Free Energies

NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage.

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements

Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-ray Scattering.

Peptide Bond Isomerization in High-Temperature Simulations.

Peptide folding simulations ⬇️

Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water.

Please, get in my way so that I can be more efficient!