C. Soares

发表

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

K. Mizuguchi, C. Deane, T. Blundell, 1999, Proteins.

Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.

C. Soares, V. Teixeira, A. Baptista, 2003, Biophysical journal.

Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

T. Blundell, H. A. Nagarajaram, J. Mendes, 2001, Biopolymers.

Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction.

J. Mendes, C. Soares, M. A. Carrondo, 1999, Biopolymers.

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

C. Soares, A. Baptista, P. Martel, 1999, Biophysical journal.

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

Bruno L. Victor, C. Soares, A. Baptista, 2013, Journal of chemical theory and computation.

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

C. Soares, M. Oliveira, I. A. Abreu, 2018, Biochimica et biophysica acta. Molecular cell research.

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

C. Soares, M. A. Carrondo, A. Baptista, 2003, Proteins.

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

C. Soares, L. Hemmingsen, S. Pires, 2012, Inorganic chemistry.

Computer assisted simulations and molecular graphics methods in molecular design 2. Proteinases and receptor and transport proteins

O. Tapia, C. Soares, R. Garratt, 1994 .

Computer assisted simulations and molecular graphics methods in molecular design

O. Tapia, C. Soares, O. Tapia, 1994 .

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

C. Soares, Bárbara Abreu, emanuel. lopes, 2020, Proteins.

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

C. Soares, V. Teixeira, A. Baptista, 2006, Biophysical journal.

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

Manuela M. Pereira, C. Soares, P. Hildebrandt, 2008, The Biochemical journal.

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.

C. Soares, B. Ludwig, A. Konstantinov, 2005, Biochemistry.

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

Filipa L. Sousa, C. Soares, D. Lousa, 2018, Nature Communications.

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

C. Soares, A. Baptista, A. S. Oliveira, 2011, Proteins.

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

C. Soares, A. Baptista, P. Hildebrandt, 2005, Biophysical journal.

Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms

C. Soares, M. Amaral, D. Sheppard, 2006, Proceedings of the National Academy of Sciences.

Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase.

Bruno L. Victor, C. Soares, M. A. Carrondo, 2016, Journal of molecular biology.

Perturbation-Relaxation Molecular Dynamics Simulations as a Tool to Explore Conformational Space. Reversible Response of the L3 Loop in Porin Towards Charge Screening Effects

O. Tapia, C. Soares, J. Björkstén, 1995 .

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

C. Soares, A. Baptista, D. Lousa, 2013, Physical chemistry chemical physics : PCCP.

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

Bruno M. Fonseca, C. Soares, R. Louro, 2013, The Biochemical journal.

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

Bruno M. Fonseca, C. Soares, R. Louro, 2009, JBIC Journal of Biological Inorganic Chemistry.

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

Bruno L. Victor, A. Laio, C. Soares, 2016, Scientific Reports.

Nickel–Iron–Selenium Hydrogenases – An Overview

C. Soares, P. Matias, I. Pereira, 2011 .

Theoretical Identiﬁcation of Proton Channels in the Quinol Oxidase aa 3 from Acidianus ambivalens

Bruno L. Victor, C. Soares, A. Baptista, 2004 .

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

C. Soares, V. Teixeira, A. Baptista, 2001, JBIC Journal of Biological Inorganic Chemistry.

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

Filipe M. Sousa, Manuela M. Pereira, C. Soares, 2017, Biochimica et biophysica acta. Bioenergetics.

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

C. Soares, M. A. Carrondo, M. Archer, 2015, Biochemistry.

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

C. Soares, V. Teixeira, Carla S. A. Baltazar, 2012, JBIC Journal of Biological Inorganic Chemistry.

The role of Lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore.

C. Soares, Y. Astier, Elisa J. Campos, 2012, Langmuir : the ACS journal of surfaces and colloids.

Reorganization and conformational changes in the reduction of tetraheme cytochromes.

C. Soares, V. Teixeira, A. Baptista, 2005, Biophysical journal.

Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures

C. Soares, M. Castanho, D. Lousa, 2022, ACS chemical biology.

Genomic evolution towards azole resistance in Candida glabrata clinical isolates unveils the importance of CgHxt4/6/7 in azole accumulation

Miguel C. Teixeira, C. Soares, A. Rodrigues, 2022, Communications Biology.

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

C. Soares, N. Micaêlo, C. M. Soares, 2008, The journal of physical chemistry. B.

Amino acids 484 and 494 of SARS-CoV-2 spike are hotspots of immune evasion affecting antibody but not ACE2 binding

Z. Ning, C. Soares, J. Demengeot, 2021, bioRxiv.

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

C. Soares, A. Baptista, J. Damas, 2014, Journal of chemical theory and computation.

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

C. Soares, L. O. Martins, P. Lindley, 2010, BMC Structural Biology.

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

C. Soares, M. A. Carrondo, P. Matias, 2005, Progress in biophysics and molecular biology.

Constant-pH molecular dynamics using stochastic titration

C. Soares, V. Teixeira, A. Baptista, 2002 .

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

Ana C. Coelho, C. Soares, N. Santos, 2018, PloS one.

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

C. Soares, A. Neves, H. Santos, 2007, The FEBS journal.

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

C. Soares, A. L. Lacey, I. Pereira, 2013, JBIC Journal of Biological Inorganic Chemistry.

Molecular and Biochemical Characterization of a Highly Stable Bacterial Laccase That Occurs as a Structural Component of theBacillus subtilis Endospore Coat*

Manuela M. Pereira, C. Soares, M. Teixeira, 2002, The Journal of Biological Chemistry.

Effect of immobilization support, water activity, and enzyme ionization state on cutinase activity and enantioselectivity in organic media

C. Soares, J. Cabral, S. Barreiros, 2004, Biotechnology and bioengineering.

A robust metallo‐oxidase from the hyperthermophilic bacterium Aquifex aeolicus

Manuela M. Pereira, R. Huber, C. Soares, 2007, The FEBS journal.

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

K S Wilson, Z Dauter, C. Soares, 1995, Structure.

The Importance of Lipid Conjugation on Anti-Fusion Peptides against Nipah Virus

C. Soares, N. Santos, Patrícia M Silva, 2022, Biomedicines.

Molecular determinants for FMN‐binding in Desulfovibrio gigas flavoredoxin

C. Rodrigues-Pousada, C. Soares, S. Mayhew, 2007, FEBS letters.

A Biochemical and Molecular Characterization of LEP1, an Extensin Peroxidase from Lupin*

C. Soares, C. Pinheiro, C. Ricardo, 2003, Journal of Biological Chemistry.

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

Margarida Casal, Artur Cavaco-Paulo, Cláudio M Soares, 2007, Journal of biotechnology.

Nine‐Heme Cytochrome c

C. Soares, M. A. Carrondo, P. Matias, 2006 .

Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase

Bruno L. Victor, C. Rodrigues-Pousada, C. Soares, 2003, JBIC Journal of Biological Inorganic Chemistry.

Gene Cluster of Rhodothermus marinusHigh-Potential Iron-Sulfur Protein:Oxygen Oxidoreductase, acaa3-Type Oxidase Belonging to the Superfamily of Heme-Copper Oxidases

Manuela M. Pereira, C. Soares, M. Teixeira, 2001, Journal of bacteriology.

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

C. Soares, V. Teixeira, Carla S. A. Baltazar, 2012, JBIC Journal of Biological Inorganic Chemistry.

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

C. Soares, S. C. Viegas, C. Arraiano, 2022, Microorganisms.

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

J. Mendes, C. Soares, A. Baptista, 1999, Proteins.

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

António M. Baptista, Cláudio M. Soares, Bruno L. Victor, 2012, J. Chem. Inf. Model..

Evolution of the thyroid hormone-binding protein, transthyretin.

J. Mendes, C. Soares, D. Power, 2000, General and comparative endocrinology.

Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

Z. Ning, C. Soares, J. Demengeot, 2021, PLoS pathogens.

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

C. Soares, M. Teixeira, A. Coelho, 2005, JBIC Journal of Biological Inorganic Chemistry.

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

R. Huber, C. Soares, R. Pogni, 2010, The FEBS journal.

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

Bruno M. Fonseca, C. Soares, R. Louro, 2015, Front. Microbiol..

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

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

Manuela M. Pereira, J. Mendes, C. Soares, 1999, Biochimica et biophysica acta.

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 c3

C. Soares, P. Matias, A. Coelho, 1999, JBIC Journal of Biological Inorganic Chemistry.

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

C. Soares, J. Damas, L. O. Martins, 2012, Acta crystallographica. Section D, Biological crystallography.

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

C. Soares, N. Micaêlo, C. M. Soares, 2007, The FEBS journal.

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

C. Soares, V. Teixeira, A. Baptista, 2005, Biophysical journal.

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

Bruno L. Victor, C. Soares, V. Teixeira, 2005, The journal of physical chemistry. B.

Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins

C. Soares, António M. Baptista and, C. M. Soares, 2001 .

SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

C. Soares, D. Lousa, Luís Borges-Araújo, 2021, bioRxiv.

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

C. Soares, V. Teixeira, A. Baptista, 2004, Biophysical journal.

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

C. Soares, M. Teixeira, L. M. Saraiva, 2015, FEBS letters.

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

C. Soares, M. Serrano, A. Henriques, 2018, Journal of bacteriology.

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

C. Soares, A. Baptista, P. Halling, 2012, The journal of physical chemistry. B.

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

António M. Baptista, Cláudio M. Soares, Diana Lousa, 2012, J. Chem. Inf. Model..

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

P. Altevogt, C. Soares, V. Morais, 2008, Biochimica et biophysica acta.

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

C. Soares, A. Baptista, M. Machuqueiro, 2010, The journal of physical chemistry. B.

Functional Domains of the Bacillus subtilis Transcription Factor AraR and Identification of Amino Acids Important for Nucleoprotein Complex Assembly and Effector Binding

C. Soares, L. J. Mota, I. S. Franco, 2006, Journal of bacteriology.

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

Filipe M. Sousa, Manuela M. Pereira, C. Soares, 2018, Redox biology.

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

António M. Baptista, Sara R. R. Campos, Pedro R. Magalhães, 2017, J. Chem. Inf. Model..

Simulation of multihaem cytochromes

C. Soares, A. Baptista, C. M. Soares, 2012, FEBS letters.

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

Manuela M. Pereira, C. Soares, A. Baptista, 2004, JBIC Journal of Biological Inorganic Chemistry.

Redox-Bohr and Other Cooperativity Effects in the Nine-heme Cytochrome c from Desulfovibrio desulfuricans ATCC 27774

C. Soares, M. A. Carrondo, V. Teixeira, 2003, Journal of Biological Chemistry.

Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome*

C. Soares, M. A. Carrondo, A. Baptista, 2001, The Journal of Biological Chemistry.

Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas

Bruno L. Victor, C. Soares, N. Micaêlo, 2008, Proteins.

Molecular Dynamics Simulations Suggest a Possible Role for NO in the Polyol Synthesis of Silver Nanostructures

C. Soares, M. Meneghetti, J. D. Da Silva, 2020, The Journal of Physical Chemistry C.

Role of the Anti-Sigma Factor SpoIIAB in Regulation of σG during Bacillus subtilis Sporulation

C. Soares, M. Serrano, A. Henriques, 2004, Journal of bacteriology.

Role of the Anti-Sigma Factor SpoIIAB in Regulation of (cid:2) G during Bacillus subtilis Sporulation

C. Soares, M. Serrano, A. Henriques, 2004 .

New targets for drug design: importance of nsp14/nsp10 complex formation for the 3’‐5’ exoribonucleolytic activity on SARS‐CoV‐2

C. Soares, S. C. Viegas, C. Arraiano, 2021, bioRxiv.

Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA.

C. Soares, C. Glaubitz, H. Kaur, 2018, Journal of the American Chemical Society.

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

C. Soares, A. Baptista, A. S. Oliveira, 2016, Biochimica et biophysica acta.

Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

António M. Baptista, A. Sofia F. Oliveira, Cláudio M. Soares, 2014, PLoS Comput. Biol..

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

Bruno L. Victor, C. Soares, A. Baptista, 2004, Biophysical journal.

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

C. Soares, M. A. Carrondo, P. Lindley, 2014, JBIC Journal of Biological Inorganic Chemistry.

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

C. Soares, L. J. Mota, I. S. Franco, 2007, Nucleic acids research.

Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods

C. Soares, M. A. Carrondo, A. Baptista, 1999, JBIC Journal of Biological Inorganic Chemistry.

Tetraheme Cytochromes C3

C. Soares, M. A. Carrondo, R. Louro, 2011 .

Hydration Effects on Enzyme Properties in Nonaqueous Media Analyzed by MD Simulations

C. Soares, A. Baptista, D. Lousa, 2016 .

Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases

C. Soares, D. Lousa, T. M. Barbosa, 2020, Scientific Reports.

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

C. Soares, W. Hinrichs, S. Panjikar, 2013, Acta crystallographica. Section D, Biological crystallography.

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

C. Soares, V. Teixeira, A. Baptista, 2008, Proteins.

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

António M. Baptista, Joaquim Mendes, Cláudio M. Soares, 2001, J. Comput. Aided Mol. Des..

The Mechanism of Superoxide Scavenging byArchaeoglobus fulgidus Neelaredoxin*

C. Soares, I. A. Abreu, M. Teixeira, 2001, The Journal of Biological Chemistry.

[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 Å and modelling studies of its interaction with the tetrahaem cytochrome c3

C. Soares, P. Matias, L. M. Saraiva, 2000, JBIC Journal of Biological Inorganic Chemistry.

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

J. Mendes, C. Soares, M. A. Carrondo, 1998, Biophysical journal.

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

Bruno M. Fonseca, C. Soares, R. Louro, 2014, Front. Microbiol..

Crystal Structure of Cardosin A, a Glycosylated and Arg-Gly-Asp-containing Aspartic Proteinase from the Flowers ofCynara cardunculus L.*

C. Soares, J. Cooper, C. Frazão, 1999, The Journal of Biological Chemistry.

The Bsmoc group as a novel scaffold for the design of irreversible inhibitors of cysteine proteases.

C. Soares, R. Guedes, R. Moreira, 2006, Bioorganic & medicinal chemistry letters.

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

C. Soares, R. Louro, C. Frazão, 2017, Biochimica et biophysica acta. Bioenergetics.

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

C. Soares, M. Fernandes, A. Cavaco‐Paulo, 2012, Proteins.

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex

António M. Baptista, A. Sofia F. Oliveira, Cláudio M. Soares, 2011, PLoS Comput. Biol..

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

C. Soares, A. Baptista, J. Damas, 2011, Protein science : a publication of the Protein Society.

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

Bruno L. Victor, C. Soares, A. Baptista, 2009, JBIC Journal of Biological Inorganic Chemistry.

Theoretical studies on the redox-Bohr effect in cytochrome c3 from Desulfovibrio vulgaris Hildenborough

C. Soares, M. A. Carrondo, P. Martel, 1997, JBIC Journal of Biological Inorganic Chemistry.

Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

C. Soares, A. Baptista, M. Castanho, 2020, Scientific Reports.

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

Filipe M. Sousa, Manuela M. Pereira, C. Soares, 2017, Scientific Reports.

Self-Assembly Molecular Dynamics Simulations Shed Light into the Interaction of the Influenza Fusion Peptide with a Membrane Bilayer

Bruno L Victor, Diana Lousa, Jorge M Antunes, 2015, J. Chem. Inf. Model..

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

Filipe M. Sousa, Manuela M. Pereira, C. Soares, 2017 .