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List of works by António M. Baptista

A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies ⬇️

scientific article published on July 18, 2013

A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method

scientific article published on 03 April 2019

A study of the contribution of changes in the cerebral blood volume to the haemodynamic response to anoxia in rat brain

scientific article

Acidic range titration of HEWL using a constant-pH molecular dynamics method

scientific article published in July 2008

Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations ⬇️

scientific article published on January 30, 2012

Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin

scientific article published on 16 February 2022

Characterization of the protein unfolding processes induced by urea and temperature

scientific article

Comparative redox and pK a calculations on cytochrome c 3 from several Desulfovibrio species using continuum electrostatic methods

Conformational analysis in a multidimensional energy landscape: study of an arginylglutamate repeat.

scientific article published in December 2009

Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein

scientific article

Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: putative correlation toward receptor docking

scientific article published in February 2006

Conformational changes induced by ATP‐hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter ⬇️

scientific article published on April 12, 2011

Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome

scientific article

Constant-pH MD Simulations Portray the Protonation and Structural Behavior of Four Decapeptides Designed to Coordinate Cu(2+).

scientific article published on 26 January 2016

Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers

scientific article published on 20 November 2015

Constant-pH MD Simulations of an Oleic Acid Bilayer

scientific article published on 27 April 2015

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein ⬇️

scientific article published on 01 October 2010

Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer

scientific article published on May 2015

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine

scientific article published in February 2006

Correction to "Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study"

scientific article published on 23 December 2014

Correction to “Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin”

scientific article published on 29 June 2022

Correction: Photonic Activation of Plasminogen Induced by Low Dose UVB.

scientific article published on 11 December 2015

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations.

scientific article published on 28 March 2016

Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas

scientific article published in April 2009

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study

scientific article published on 18 January 2017

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies

scientific article published on 11 March 2005

Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site

scientific article (publication date: December 2014)

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

scientific article published on August 2001

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

scientific article published on 01 December 1999

Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796

scientific article published on 01 April 2010

Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex

scientific article

Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations

scientific article

Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase

scientific article published on 23 December 2003

Is the prediction of pKavalues by constant‐pH molecular dynamics being hindered by inherited problems? ⬇️

scientific article published on August 30, 2011

Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations

scientific article published on September 2010

Modeling the partitioning of amino acids in aqueous two phase systems

scientific article published on 16 December 2013

Molecular Anatomy of Plant Photoprotective Switches: The Sensitivity of PsbS to the Environment, Residue by Residue

article

Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6

scientific article

Molecular dynamics at constant pH and reduction potential: application to cytochrome c(3)

article

Natural Domain Design: Enhanced Thermal Stability of a Zinc-Lacking Ferredoxin Isoform Shows that a Hydrophobic Core Efficiently Replaces the Structural Metal Site†

scientific article published on 01 August 2006

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

scientific article published on 01 August 2005

Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field

scientific article published on 01 July 2006

Pathways of H2 toward the active site of [NiFe]-hydrogenase

scientific article published on 26 May 2006

Photonic activation of plasminogen induced by low dose UVB.

scientific article

Predicting protein partition coefficients in aqueous two phase system

scientific article published in October 2016

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model.

scientific article published on 11 October 2013

Predicting the partition coefficients of a recombinant cutinase in polyethylene glycol/phosphate aqueous two-phase systems

scientific article published on 01 November 1997

Progress in the prediction of pKa values in proteins

scientific article published on 15 October 2011

Proton pathways in a [NiFe]-hydrogenase: A theoretical study

scientific article published on 01 February 2008

Protonation of DMPC in a Bilayer Environment Using a Linear Response Approximation

scientific article published on 01 May 2014

Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases?

scientific article published on 7 December 2007

Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies

scientific article (publication date: 19 September 2003)

Reorganization and conformational changes in the reduction of tetraheme cytochromes

scientific article published on 16 September 2005

Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations

scientific article published on March 2004

Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations.

scientific article

Simulation of multihaem cytochromes ⬇️

scientific article published on October 19, 2011

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

scientific article published on 01 April 1997

Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus ⬇️

scientific article published on November 9, 2012

Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB.

scientific article

Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents ⬇️

scientific article published on February 1, 2011

Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study

scientific article published on 24 October 2013

Structuring Peptide Dendrimers Through pH Modulation and Substrate Binding

scientific article

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

scientific article published on 20 September 2001

The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics.

scientific article published on 23 September 2015

The Pathway for O2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family

scientific article published on 01 August 2014

The anti-inflammatory action of the analgesic kyotorphin neuropeptide derivatives: insights of a lipid-mediated mechanism.

scientific article published on 7 September 2015

The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - comparative modeling to probe the molecular basis

scientific article published on 18 October 2007

The origin of trypsin: evidence for multiple gene duplications in trypsins.

scientific article published in September 1998

The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study

scientific article

Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens

scientific article published on 17 September 2004

Thermodynamic Redox Behavior of the Heme Centers ofcbb3Heme-Copper Oxygen Reductase fromBradyrhizobium japonicum

scientific article published in 2008

Thermodynamic Redox Behavior of the Heme Centers ofcbb3Heme-Copper Oxygen Reductase fromBradyrhizobium japonicum†

scientific article published on 27 October 2007

Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies

scientific article published on August 2008

Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers

scientific article published on 13 November 2014

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

scientific article published on 15 March 2011

Water dependent properties of cutinase in nonaqueous solvents: a computational study of enantioselectivity

scientific article published on 27 May 2005

Water encapsulation in a polyoxapolyaza macrobicyclic compound.

scientific article

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