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List of works by Cláudio M. Soares

A LysM Domain Intervenes in Sequential Protein-Protein and Protein-Peptidoglycan Interactions Important for Spore Coat Assembly in Bacillus subtilis

scientific article published on 28 January 2019

A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies

scientific article published on 18 July 2013

A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus

scientific article published on 19 April 2007

Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin

scientific article

An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation

scientific article published in Nature Communications

An iterative structure-assisted approach to sequence alignment and comparative modeling

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

scientific article published on January 30, 2012

Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1

scientific article published on 29 June 2015

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

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

scientific article published on 28 March 2016

Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding.

scientific article

Design of a peptidic turn with high affinity for Hg(II)

scientific article published on 17 October 2012

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

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

scientific article published in July 1999

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)

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space

scientific article

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

scientific article published on 17 July 2019

Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding.

scientific article published on April 2006

Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme.

scientific article

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

scientific article published on 15 June 2016

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase.

scientific article published in October 2005

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

Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases

scientific article

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

scientific article published on 01 April 2010

Insights into the structure of the diiron site of RIC from Escherichia coli.

scientific article published on 9 January 2015

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

Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome c 553 from D. vulgaris

scientific article published in November 2000

Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

scientific article

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

scientific article published on September 2010

Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1

scientific article published on 01 January 2013

Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3).

scientific article published on May 2004

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

scientific article published on 01 May 2007

Molecular Dynamics Simulation of Cytochrome c3: Studying the Reduction Processes Using Free Energy Calculations ⬇️

scientific article published on April 1, 1998

Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat.

scientific article published on 7 March 2002

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 determinants for FMN-binding in Desulfovibrio gigas flavoredoxin.

scientific article

Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results

scientific article published on 01 March 2012

Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2.

scientific article published on 28 July 2017

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

Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 : primary sequence determination, crystallographic refinement at 1.8  and modelling studies of its interaction with the tetrahaem cytochrome c 3

scientific article published in August 1999

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

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

scientific article published on 11 October 2013

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon

scientific article published on 7 July 2007

Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies.

scientific article

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

scientific article published on 01 February 2008

Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants

scientific article

Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX

scientific article published in September 2013

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)

Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus

scientific article published on 17 February 2018

Reorganization and conformational changes in the reduction of tetraheme cytochromes

scientific article published on 16 September 2005

Role of the anti-sigma factor SpoIIAB in regulation of sigmaG during Bacillus subtilis sporulation

scientific article

Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion Peptide with a membrane bilayer.

scientific article published on 13 April 2015

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

scientific article published on June 1999

Simulation of multihaem cytochromes ⬇️

scientific article published on October 19, 2011

Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae.

scientific article published on 18 May 2011

Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases

scientific article

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

scientific article published on November 9, 2012

Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking

scientific article

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

scientific article published on 9 February 2017

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 features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach

scientific article published on 01 April 2012

Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase

scientific article

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

scientific article published on 20 September 2001

Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods

scientific article published in PLoS ONE

Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview

scientific article

Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers.

scientific article published on 14 January 2007

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

scientific article published on 01 August 2014

The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α-Hemolysin Nanopore

scientific article published on 24 October 2012

The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel

scientific article published on 01 September 1999

The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis

scientific article

The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.

scientific article

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 multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity.

scientific article

The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs

scientific article published in 2022

The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications

scientific article published on 31 October 2017

The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton-transfer mechanism

scientific article

The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes

scientific article published on 2 December 2008

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

scientific article published on 17 September 2004

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

scientific article published on 27 May 2005

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