List of works - Sérgio F. Sousa

A Flow Cytometric and Computational Approaches to Carbapenems Affinity to the Different Types of Carbapenemases

scientific article

A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems

scientific article published in 2022

A Molecular Perspective on Sirtuin Activity

scientific article published on 15 November 2020

A comparative molecular dynamics study on the complexation of alkali metal cations by a poly-ethylene-glycol type podand in water and in dichloromethane

An Atomic-Level Perspective of HMG-CoA-Reductase: The Target Enzyme to Treat Hypercholesterolemia

scientific article published on 26 August 2020

Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns

article

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

scientific article published in September 2016

Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors

article

Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble.

scientific article

Chemically Modified Tetracyclines as Inhibitors of MMP-2 Matrix Metalloproteinase: A Molecular and Structural Study

scientific article published on 09 November 2012

Classification study of solvation free energies of organic molecules using machine learning techniques

scholarly article by N. S. Hari Narayana Moorthy et al published 2014 in RSC Advances

Comparative Assessment of Theoretical Methods for the Determination of Geometrical Properties in Biological Zinc Complexes

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes.

scientific article published on 25 June 2013

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

article

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules ⬇️

scientific article published on 01 March 2013

Complexation of alkali metal cations by crown-ether type podands with applications in solvent extraction: insights from quantum chemical calculations

scientific article published on 04 March 2011

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI.

scientific article published on 25 February 2013

Computational enzymatic catalysis--clarifying enzymatic mechanisms with the help of computers

scientific article published on 06 August 2012

Crown-Ether Type Podands as Alkali Metal Cation Extractants: Influence of the Number of Oxygens in the Chain

Current Status of the Use of Multifunctional Enzymes as Anti-Cancer Drug Targets

scientific article published in 2021

Decomplexation and complexation of alkali metal cations by a crown-ether-type podand in dichloromethane: a steered molecular dynamics study

Dehydration of a polyether type extraction agent and of the corresponding K+ complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods

scientific article published on 26 June 2012

Detailed Atomistic Analysis of the HIV-1 Protease Interface

article

Detection of farnesyltransferase interface hot spots through computational alanine scanning mutagenesis.

scientific article published on 2 December 2011

Direct covalent modification as a strategy to inhibit nuclear factor-kappa B.

scientific article published on January 2009

Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism

Enzymatic “tricks”: Carboxylate shift and sulfur shift

Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation

Factors influencing the binding of a potassium cation to a polyethylene glycol type podand in liquid–liquid extraction—a molecular dynamics study

Farnesyltransferase inhibitors: a comprehensive review based on quantitative structural analysis.

scientific article

Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem

scientific article published on January 2008

Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism

scientific article

Farnesyltransferase: Theoretical studies on peptide substrate entrance—thiol or thiolate coordination?

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

scientific article published on 04 July 2019

Gas-phase geometry optimization of biological molecules as a reasonable alternative to a continuum environment description: fact, myth, or fiction?

scientific article published in December 2009

General performance of density functionals

scientific article published on 25 August 2007

HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).

scientific article published on 18 August 2016

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives.

scientific article published on 4 October 2017

In Silico–Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects

article

In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors

scientific article published on 01 September 2012

Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC

Molecular Dynamics Analysis of FAAH Complexed with Anandamide

scientific article published in 2015

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

scientific article published on 18 February 2016

Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif

article

Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior

article

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

scientific article

New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation

scientific article published on 21 October 2021

New designs for MRI contrast agents.

scientific article published in July 2003

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

scientific article

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field.

scientific article published on August 2014

Protein-ligand docking: current status and future challenges

scientific article published on October 2006

Receptor-based virtual screening protocol for drug discovery.

scientific article published on June 2015

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

article published in 2015

Structural Characterization of Membrane Protein Dimers

scientific article published on 01 January 2019

Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs).

scientific article published on 15 October 2013

Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins

scientific article published on 01 April 2019

Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors

Study of human salivary proline-rich proteins interaction with food tannins.

scientific article published on 19 September 2017

The Biofilms Structural Database

scientific article published on 05 May 2020

The Buzz on Insecticides: A Review of Uses, Molecular Structures, Targets, Adverse Effects, and Alternatives

scientific article published in 2023

The Zinc proteome: a tale of stability and functionality

The carboxylate shift in zinc enzymes: a computational study

scientific article published in February 2007

The search for the mechanism of the reaction catalyzed by farnesyltransferase

scientific article published in January 2009

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere

article

Theoretical studies on farnesyltransferase: The distances paradox explained

scholarly article by Sérgio F. Sousa published in October 2006

Transfer of the K+ Cation Across a Water/Dichloromethane Interface: A Steered Molecular Dynamics Study with Implications in Cation Extraction

scientific article published on 08 February 2012

Transport Properties of Light Gases in Nanochannels of L-Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations

scientific article

Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase

Unraveling the mechanism of the farnesyltransferase enzyme

scientific article

VMD Store-A VMD Plugin to Browse, Discover, and Install VMD Extensions

scientific article published on 04 November 2019

Virtual Screening of Compound Libraries ⬇️

scientific article published on January 1, 2009

Virtual screening in drug design and development.

scientific article

List of works by Sérgio F. Sousa

A Flow Cytometric and Computational Approaches to Carbapenems Affinity to the Different Types of Carbapenemases

A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems

A Molecular Perspective on Sirtuin Activity

A comparative molecular dynamics study on the complexation of alkali metal cations by a poly-ethylene-glycol type podand in water and in dichloromethane

An Atomic-Level Perspective of HMG-CoA-Reductase: The Target Enzyme to Treat Hypercholesterolemia

Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors

Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble.

Chemically Modified Tetracyclines as Inhibitors of MMP-2 Matrix Metalloproteinase: A Molecular and Structural Study

Classification study of solvation free energies of organic molecules using machine learning techniques

Comparative Assessment of Theoretical Methods for the Determination of Geometrical Properties in Biological Zinc Complexes

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules ⬇️

Complexation of alkali metal cations by crown-ether type podands with applications in solvent extraction: insights from quantum chemical calculations

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI.

Computational enzymatic catalysis--clarifying enzymatic mechanisms with the help of computers

Crown-Ether Type Podands as Alkali Metal Cation Extractants: Influence of the Number of Oxygens in the Chain

Current Status of the Use of Multifunctional Enzymes as Anti-Cancer Drug Targets

Decomplexation and complexation of alkali metal cations by a crown-ether-type podand in dichloromethane: a steered molecular dynamics study

Dehydration of a polyether type extraction agent and of the corresponding K+ complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods

Detailed Atomistic Analysis of the HIV-1 Protease Interface

Detection of farnesyltransferase interface hot spots through computational alanine scanning mutagenesis.

Direct covalent modification as a strategy to inhibit nuclear factor-kappa B.

Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism

Enzymatic “tricks”: Carboxylate shift and sulfur shift

Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation

Factors influencing the binding of a potassium cation to a polyethylene glycol type podand in liquid–liquid extraction—a molecular dynamics study

Farnesyltransferase inhibitors: a comprehensive review based on quantitative structural analysis.

Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem

Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism

Farnesyltransferase: Theoretical studies on peptide substrate entrance—thiol or thiolate coordination?

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Gas-phase geometry optimization of biological molecules as a reasonable alternative to a continuum environment description: fact, myth, or fiction?

General performance of density functionals

HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives.

In Silico–Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects

In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors

Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC

Molecular Dynamics Analysis of FAAH Complexed with Anandamide

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif

Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation

New designs for MRI contrast agents.

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field.

Protein-ligand docking: current status and future challenges

Receptor-based virtual screening protocol for drug discovery.

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

Structural Characterization of Membrane Protein Dimers

Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs).

Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins

Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors

Study of human salivary proline-rich proteins interaction with food tannins.

The Biofilms Structural Database

The Buzz on Insecticides: A Review of Uses, Molecular Structures, Targets, Adverse Effects, and Alternatives

The Zinc proteome: a tale of stability and functionality

The carboxylate shift in zinc enzymes: a computational study

The search for the mechanism of the reaction catalyzed by farnesyltransferase

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere

Theoretical studies on farnesyltransferase: The distances paradox explained

Transfer of the K+ Cation Across a Water/Dichloromethane Interface: A Steered Molecular Dynamics Study with Implications in Cation Extraction

Transport Properties of Light Gases in Nanochannels of L-Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations

Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase

Unraveling the mechanism of the farnesyltransferase enzyme

VMD Store-A VMD Plugin to Browse, Discover, and Install VMD Extensions

Virtual Screening of Compound Libraries ⬇️

Virtual screening in drug design and development.