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Lista de obras de Maria J. Ramos

A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale

A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase

article

A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans

artículo científico publicado en 2018

A QM/MM study of the reaction mechanism of human β-ketoacyl reductase.

artículo científico publicado en 2016

A comparative density-functional study of the reaction mechanism of the O2-dependent coproporphyrinogen III oxidase

artículo científico publicado en 2008

A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones

scientific article published on 25 May 2019

A molecular modeling study of inhibitors of nuclear factor kappa-B (p50)--DNA binding

artículo científico publicado en 2003

A new device for treatment of persistent otitis media with effusion

artículo científico publicado en 2013

A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy

artículo científico publicado en 2014

A new strategy to model the Si(100) surface

article

A novel synthetic peptide inspired on Lys49 phospholipase A2 from Crotalus oreganus abyssus snake venom active against multidrug-resistant clinical isolates.

artículo científico publicado en 2018

A tale of two acids: when arginine is a more appropriate acid than H3O+.

artículo científico publicado en 2010

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains

artículo científico publicado en 2011

Adsorption of protected and unprotected amino-cyclopentene at the Si(100) surface modeled with a hybrid quantum mechanical cluster technique

scholarly article in Physical Review B, vol. 72 no. 7, August 2005

Amino acid deprivation using enzymes as a targeted therapy for cancer and viral infections

artículo científico publicado en 2016

An analytic method for the calculation of electrostatic molecular potentials

Analyses of cobalt–ligand and potassium–ligand bond lengths in metalloproteins: trends and patterns

scientific article published on 22 May 2014

Analysis of the α-Glucosidase Inhibitory Activity of Chromenone Derivatives Based on their Molecular Features: A Computational Study ⬇️

artículo científico publicado el 1 de noviembre de 2011

Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds

artículo científico publicado en 2012

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

article

Anandamide targets aromatase: A breakthrough on human decidualization

artículo científico publicado en 2019

Anchoring effects in a wide binding pocket: the molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium.

artículo científico publicado en 2008

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

artículo científico publicado en 2016

Are hot-spots occluded from water?

artículo científico publicado en 2013

Aryl- and Heteroaryl-Thiosemicarbazone Derivatives and Their Metal Complexes: A Pharmacological Template

scholarly article by Narayana S.H.N. Moorthy et al published 1 May 2013 in Recent Patents on Anti-Cancer Drug Discovery

Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions

artículo científico publicado en 2020

Atomic-Level Rational Drug Design

Atomistic details of the Catalytic Mechanism of Fe(III)-Zn(II) Purple Acid Phosphatase

artículo científico publicado en 2010

AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins

artículo científico publicado en 2014

Autoinflation for treatment of persistent otitis media with effusion in children: a cross-over study with a 12-month follow-up

artículo científico publicado en 2014

Backbone Importance for Protein−Protein Binding†

artículo científico publicado en 2007

Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells

artículo científico publicado en 2019

Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds

artículo científico publicado en 2010

Benchmarking of Density Functionals for the Accurate Description of Thiol–Disulfide Exchange

artículo científico publicado en 2014

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs

artículo científico publicado en 2016

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

article

Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors

scholarly article in RSC Advances, vol. 4 no. 38, 2014

Biological evaluation, chelation, and molecular modeling studies of novel metal-chelating inhibitors of NF-kappaB-DNA binding: structure activity relationships

artículo científico publicado en 2006

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

artículo científico publicado en 2013

Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase

artículo científico publicado en 2014

Byte structure variable length coding (BS-VLC): a new specific algorithm applied in the compression of trajectories generated by molecular dynamics

artículo científico publicado en 2000

CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

artículo científico publicado en 2014

Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas

artículo científico publicado en 2016

Calculation of hyperfine coupling constants of muonated radicals

article published in 1990

Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations

artículo científico publicado en 2014

Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study

Challenges in spectroscopy: accuracy versus interpretation from isolated molecules to condensed phases

artículo científico publicado en 2019

Chemical behavior of methylpyranomalvidin-3-O-glucoside in aqueous solution studied by NMR and UV-visible spectroscopy.

artículo científico publicado en 2011

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

artículo científico publicado en 2012

Cholesterol Biosynthesis: A Mechanistic Overview.

artículo científico publicado en 2016

Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study

artículo científico publicado en 2017

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

Combined ligand and structure based binding mode analysis of oxidosqualene cyclase inhibitors

scholarly article in RSC Advances, vol. 3 no. 45, 2013

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in

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

Comparative Structural Analysis of α-Glucosidase Inhibitors on Difference Species: A Computational Study

article

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

artículo científico publicado en 2013

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

article

Comparative density functional study of models for the reaction mechanism of uroporphyrinogen III synthase

artículo científico publicado en 2008

Comparative evolutionary genomics of the HADH2 gene encoding Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)

artículo científico publicado en 2006

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI.

artículo científico publicado en 2013

Computational Characterization of the Substrate-Binding Mode in Coproporphyrinogen III Oxidase ⬇️

artículo científico publicado el 3 de febrero de 2011

Computational Enzymatic Catalysis

article published in 2008

Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5′-Phosphate-Requiring Enzymes

artículo científico publicado en 2011

Computational alanine scanning mutagenesis--an improved methodological approach

Computational analysis of ligand recognition sites of homo- and heteropentameric 5-HT3 receptors

artículo científico publicado en 2010

Computational approaches to the study of some lanthanide (III)–polyazamacrocyclic chelates for magnetic resonance imaging

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

artículo científico

Computational insight into anti-mutagenic properties of CYP1A flavonoid ligands

artículo científico publicado en 2005

Computational insights into the photochemical step of the reaction catalyzed by protochlorophylide oxidoreductase

article by Pedro Jorge Silva & Maria J. Ramos published 28 March 2011 in International Journal of Quantum Chemistry

Computational optimization of AG18051 inhibitor for amyloid-β binding alcohol dehydrogenase enzyme

Computational studies of new potential antimalarial compounds--stereoelectronic complementarity with the receptor

artículo científico publicado en 2003

Computational studies on class I ribonucleotide reductase: understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer.

artículo científico publicado en 2005

Computational studies on the reactivity of substituted 1,2-dihydro-1,2-azaborines.

artículo científico publicado en 2009

Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases

Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway

scientific article published on 11 June 2019

Conformational study of two diasteroisomers of vinylcatechin dimers in a methanol solution

Cover Feature: Different Enzyme Conformations Induce Different Mechanistic Traits in HIV‐1 Protease (Chem. Eur. J. 42/2022)

artículo científico publicado en 2022

DFT studies on the β-glycosidase catalytic mechanism: The deglycosylation step

article by Natércia F. Brás et al published April 2010 in Computational and Theoretical Chemistry

Definition of an electronic profile of compounds with inhibitory activity against hematin aggregation in malaria parasite

artículo científico publicado en 2004

Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: the role of the enzyme

artículo científico publicado en 2005

Density-Functional Study of Mechanisms for the Cofactor-Free Decarboxylation Performed by Uroporphyrinogen III Decarboxylase

Density-functional calculations of the Cu, Zn superoxide dismutase redox potential: The influence of active site distortion

Design of 2-cyclopentenone derivatives with enhanced NF-κB: DNA binding inhibitory properties

scholarly article by Pedro Alexandrino Fernandes et al published October 2004 in Computational and Theoretical Chemistry

Detailed Atomistic Analysis of the HIV-1 Protease Interface

article

Detailed microscopic study of the full zipA:FtsZ interface.

artículo científico publicado en 2006

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

artículo científico publicado en 2011

Determination of the ΔpKa between the active site cysteines of thioredoxin and DsbA

article published in 2006

Determining the glycation site specificity of human holo-transferrin

Development of ribonucleotide reductase inhibitors: a review on structure activity relationships.

artículo científico publicado en 2013

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV‐1 Protease

artículo científico publicado en 2022

Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study

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

artículo científico publicado en 2009

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes

artículo científico publicado en 2005

Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis.

artículo científico publicado en 2014

Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex.

artículo científico publicado en 2014

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

artículo científico publicado en 2014

Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates

article

Drug Permeation Across the Bacterial Membrane: Combining Theoretical and Experimental Approaches

Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead

article

DszA Catalyzes C–S Bond Cleavage through N<sup>5</sup>–Hydroperoxyl Formation

artículo científico publicado en 2024

Effect of thetert-butiloxycarbonyl protecting group on the adsorption of protected amino-cyclopentene on the Si(100) surface

scholarly article in Physical Review B, vol. 75 no. 12, March 2007

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

Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties

scientific article published on 11 June 2019

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

article

Enzymatic “tricks”: Carboxylate shift and sulfur shift

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

Enzyme Ribonucleotide Reductase: Unraveling an Enigmatic Paradigm of Enzyme Inhibition by Furanone Derivatives

Erratum to: A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase

article

Establishing the Catalytic Mechanism of Human Pancreatic α-Amylase with QM/MM Methods

artículo científico publicado en 2015

Evaluation of a flavonoids library for inhibition of pancreatic α-amylase towards a structure-activity relationship

scientific article published on 01 December 2019

Evans Blue is an inhibitor of nuclear factor-kappa B (NF-kappaB)-DNA binding

artículo científico publicado en 2004

Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase η

article published in 2019

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

artículo científico publicado en 2013

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

artículo científico publicado en 2004

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

Foreword

Fused aryl-phenazines: scaffold for the development of bioactive molecules

artículo científico publicado en 2014

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

artículo científico publicado en 2009

Gathering computational genomics and proteomics to unravel adaptive evolution

artículo científico publicado en 2007

General performance of density functionals

artículo científico publicado en 2007

Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets.

artículo científico publicado en 2016

Glutathione transferase A1-1: catalytic importance of arginine 15.

artículo científico publicado en 2010

Glutathione transferase A1-1: catalytic role of water

Glutathione transferase classes alpha, pi, and mu: GSH activation mechanism

artículo científico publicado en 2010

Glutathione transferase: new model for glutathione activation

artículo científico publicado en 2008

Glycosidase inhibitors: a patent review (2008-2013).

artículo científico publicado en 2014

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

artículo científico publicado en 2016

Hot Spot Occlusion from Bulk Water: a Comprehensive Study of the Complex between the Lysozyme HEL and the Antibody FVD1.3

artículo científico publicado en 2007

Hot spots--a review of the protein-protein interface determinant amino-acid residues

artículo científico publicado en 2007

Human ether-a-go-go-related gene channel blockers and its structural analysis for drug design.

artículo científico publicado en 2013

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.

artículo científico publicado en 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

Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein.

artículo científico publicado en 1997

Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms

artículo científico publicado en 2017

Influence of a flavan-3-ol substituent on the affinity of anthocyanins (pigments) toward vinylcatechin dimers and proanthocyanidins (copigments).

artículo científico publicado en 2012

Influence of the environment on protein bond energies

Inhibition of Pancreatic Elastase by Polyphenolic Compounds

Inhibitory activity of polyhydroxycarboxylate chelators against recombinant NF-kappaB p50 protein-DNA binding

artículo científico publicado en 2005

Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase

Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations

artículo científico publicado en 2016

Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms

artículo científico publicado en 2012

Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases

scientific article published on 07 October 2014

Insights on Resistance to Reverse Transcriptase: The Different Patterns of Interaction of the Nucleoside Reverse Transcriptase Inhibitors in the Deoxyribonucleotide Triphosphate Binding Site Relative to the Normal Substrate

Introduction

Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota,Manisspp.)

scientific article published in 2006

Isomerization of Δ5-androstene-3,17-dione into Δ4-androstene-3,17-dione catalyzed by human glutathione transferase A3-3: a computational study identifies a dual role for glutathione

artículo científico publicado en 2014

Ligand based analysis on HMG-CoA reductase inhibitors

article

MADAMM: a multistaged docking with an automated molecular modeling protocol

artículo científico publicado en 2009

Mammalian cytosolic glutathione transferases

scientific article published on August 2008

Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine

artículo científico publicado en 2004

Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes

scientific article published on 13 September 2011

Mechanism of Glutathione Transferase P1-1-Catalyzed Activation of the Prodrug Canfosfamide (TLK286, TELCYTA)

scientific article published in 2013

Mechanism of a Soluble Fumarate Reductase from Shewanella frigidimarina: A Theoretical Study

artículo científico publicado en 2006

Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues

artículo científico publicado en 2008

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations.

artículo científico publicado en 2017

Mechanistic Pathway on Human α-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations.

artículo científico publicado en 2018

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

Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase

artículo científico publicado en 2017

Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates.

artículo científico publicado en 2008

Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations

scholarly article in RSC Advances, vol. 8 no. 48, 2018

Metals in proteins: cluster analysis studies

artículo científico publicado en 2010

Microscopic detail provided for the adsorption of protected amino-cyclopentene on Si(100)

Mitochondrial introgressions into the nuclear genome of the domestic cat.

artículo científico publicado en 2007

Model structure for the human blood coagulation agent β-factor XIIa ⬇️

artículo científico publicado el 1 de junio de 1991

Modeling enzyme-inhibitor interactions in serine proteases

Modeling of Human Fatty Acid Synthase and in Silico Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains.

artículo científico publicado en 2017

Modelling beta-1,3-exoglucanase-saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall

artículo científico publicado en 2009

Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines

Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association. A molecular modeling approach on the mechanism of microtubule stabilizing agents

artículo científico publicado en 2018

Molecular Dynamics Analysis of FAAH Complexed with Anandamide

artículo científico publicado en 2015

Molecular Dynamics Model of Unliganded HIV-1 Reverse Transcriptase

article

Molecular Dynamics Simulations of Angiotensin II in Aqueous and Dimethyl Sulfoxide Environments

article

Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase

article

Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.

artículo científico publicado en 2008

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

artículo científico

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 of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme

artículo científico publicado en 2008

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

artículo científico publicado en 2009

Molecular dynamics studies on both bound and unbound renin protease ⬇️

artículo científico publicado el 25 de marzo de 2013

Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance to nucleoside analogs

artículo científico publicado en 2006

Molecular interactions between human cytochrome P450 1A2 and flavone derivatives

artículo científico publicado en 2006

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2.

artículo científico publicado en 2017

Molecular recognition of 15-deoxy-Δ12,14-prostaglandin J2 by nuclear factor-kappa B and other cellular proteins

scientific article published in 2005

Multidimensional epistasis and fitness landscapes in enzyme evolution

artículo científico publicado en 2012

Muon spin rotation spectra for muonium isotopically substituted ethyl radicals

Muonium substituted organic free radicals in liquids. Muonium—electron hyperfine, coupling constants of alkyl and allyl radicals

article

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces

artículo científico publicado en 2016

New designs for MRI contrast agents.

artículo científico publicado en 2003

New insights about the monomer and homodimer structures of the human AOX1

scientific article published on 07 June 2019

New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models

scholarly article by Gaspar P. Pinto published in September 2015

New insights into a critical biological control step of the mechanism of Ribonucleotide reductase

article by Nuno M.F.S.A. Cerqueira et al published November 2004 in Computational and Theoretical Chemistry

Nuclear factor kappa B: a potential target for anti-HIV chemotherapy

artículo científico publicado en 2003

On the modeling of snake venom serine proteinase interactions with benzamidine-based thrombin inhibitors

artículo científico publicado en 2004

Overview of ribonucleotide reductase inhibitors: an appealing target in anti-tumour therapy

artículo científico publicado en 2005

PLP undergoes conformational changes during the course of an enzymatic reaction

artículo científico publicado en 2014

Parameterization of AZT—A widely used nucleoside inhibitor of HIV-1 reverse transcriptase

article

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

artículo científico publicado en 2013

Parameters for molecular dynamics simulations of iron-sulfur proteins

artículo científico publicado en 2013

Parametrization of Molybdenum Cofactors for the AMBER Force Field

artículo científico publicado en 2018

Parametrization of Synthetic Amino Acids

Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities.

artículo científico publicado en 2015

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

artículo científico publicado en 2014

Prediction of the relationship between the structural features of andrographolide derivatives and α-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR) Study ⬇️

artículo científico publicado el 20 de diciembre de 2010

Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools ⬇️

artículo científico publicado el 8 de abril de 2013

Preface

Properties that rank protein:protein docking poses with high accuracy

artículo científico publicado en 2018

Protein-ligand docking: current status and future challenges

artículo científico publicado en 2006

Protein-protein docking dealing with the unknown

artículo científico publicado en 2010

Protein–protein recognition: a computational mutagenesis study of the MDM2–P53 complex

Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation

artículo científico publicado en 2017

Pyruvate Formate Lyase: A New Perspective

article published in 2003

QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions.

artículo científico publicado en 2010

QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme

QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA ⬇️

artículo científico publicado el 11 de noviembre de 2011

QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase

QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface

artículo científico publicado en 2006

QSAR Analysis of Isosteviol Derivatives as α-Glucosidase Inhibitors with Element Count and Other Descriptors

article

QSAR analysis of 2-benzoxazolyl hydrazone derivatives for anticancer activity and its possible target prediction

article

QSAR and pharmacophore analysis of a series of piperidinyl urea derivatives as HERG blockers and H3 antagonists

artículo científico publicado en 2013

QSAR and pharmacophore analysis of thiosemicarbazone derivatives as ribonucleotide reductase inhibitors

Re(I) and Tc(I) complexes for targeting nitric oxide synthase: influence of the chelator in the affinity for the enzyme.

artículo científico publicado en 2015

Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations

artículo científico publicado en 2014

Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations

artículo científico publicado en 2016

Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study

artículo científico publicado en 2007

Receptor-based virtual screening protocol for drug discovery.

artículo científico publicado en 2015

Receptor-drug association studies in the inhibition of the hematin aggregation process of malaria

artículo científico publicado en 2003

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

article published in 2015

Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations

article

Revisiting Partition in Hydrated Bilayer Systems

artículo científico publicado en 2017

Ribonucleotide Reductase – Computational Studies

Ribonucleotide activation by enzyme ribonucleotide reductase: understanding the role of the enzyme.

artículo científico publicado en 2004

Ribonucleotide reductase: a critical enzyme for cancer chemotherapy and antiviral agents

artículo científico publicado en 2007

Ribonucleotide reductase: a mechanistic portrait of substrate analogues inhibitors.

artículo científico publicado en 2010

Role of the variable active site residues in the function of thioredoxin family oxidoreductases.

artículo científico publicado en 2009

Similarities and differences in the thioredoxin superfamily

artículo científico publicado en 2005

Structural Analysis of 2-Piperidin-4-yl-Actamide Derivatives for hERG Blocking and MCH R1 Antagonistic Activities ⬇️

artículo científico publicado el 1 de marzo de 2012

Structural Specificity of Flavonoids in the Inhibition of Human Fructose 1,6-Bisphosphatase

artículo científico publicado en 2020

Structural analysis of ABAD point mutations causing 2-methyl-3-hydroxylbutyryl-coA deficiency

Structural analysis of structurally diverse α-glucosidase inhibitors for active site feature analysis

artículo científico publicado el 8 de septiembre de 2011

Structural analysis of α-glucosidase inhibitors by validated QSAR models using topological and hydrophobicity based descriptors

article

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

artículo científico publicado en 2013

Structural and functional implications of positive selection at the primate angiogenin gene

artículo científico publicado en 2007

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

scientific article published on 01 April 2019

Structural basis for the GSK-3beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1H-[1,2,3] triazole-4-carboxylic acid derivatives

artículo científico publicado en 2005

Structural characterization of a A-type linked trimeric anthocyanin derived pigment occurring in a young Port wine.

artículo científico publicado en 2013

Structural characterization of inclusion complexes between cyanidin-3-O-glucoside and β-cyclodextrin

artículo científico publicado en 2013

Structural divergence and adaptive evolution in mammalian cytochromes P450 2C

article

Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors

Structural features of copigmentation of oenin with different polyphenol copigments

artículo científico publicado en 2013

Structural insight on the activity of type 1 angiotensin II peptide antagonists using MD simulations

artículo científico publicado en 2008

Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement.

artículo científico publicado en 2016

Structure, Dynamics, and Energetics of ATP Hydrolysis by ABC Transporters

Studies of inclusion complexes between cyclodextrins and polyazamacrocyclic chelates of lanthanide (III) ions

Studies on neuraminidase inhibition

Studies on α-glucosidase inhibitors development: magic molecules for the treatment of carbohydrate mediated diseases.

artículo científico

Substrate recognition in HIV-1 protease: a computational study.

artículo científico publicado en 2010

Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

article

Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(μ-N(t)Bu)]2 (E = O, S, and Se) Cyclodiphosphazanes

artículo científico publicado en 2015

Synthesis and structural characterization of two diasteroisomers of vinylcatechin dimers

artículo científico publicado en 2009

The Accuracy of Density Functional Theory in the Description of Cation-π and π-Hydrogen Bond Interactions

artículo científico publicado en 2011

The Catalytic Mechanism of Carboxylesterases: A Computational Study

artículo científico publicado en 2014

The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations

article

The Catalytic Mechanism of RNA Polymerase II.

artículo científico publicado en 2011

The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac

scientific article published on 08 July 2016

The Catalytic Mechanism of the Pyridoxal-5'-phosphate-Dependent Enzyme, Histidine Decarboxylase: A Computational Study.

artículo científico publicado en 2017

The First Mammalian Aldehyde Oxidase Crystal Structure: INSIGHTS INTO SUBSTRATE SPECIFICITY

artículo científico publicado en 2012

The Protein kinase inhibitor balanol: structure-activity relationships and structure-based computational studies.

artículo científico publicado en 2008

The Role of Hypernetworks as a Multilevel Methodology for Modelling and Understanding Dynamics of Team Sports Performance

scientific article published on 01 September 2019

The Sulfur Shift: An Activation Mechanism for Periplasmic Nitrate Reductase and Formate Dehydrogenase

article published in 2013

The Zinc proteome: a tale of stability and functionality

The adaptive evolution of the mammalian mitochondrial genome

artículo científico publicado en 2008

The barriers to internal rotation for muonic-substituted ethyl radicals

The carboxylate shift in zinc enzymes: a computational study

artículo científico publicado en 2007

The catalytic mechanism of mouse renin studied with QM/MM calculations ⬇️

artículo científico publicado el 13 de julio de 2012

The catalytic mechanism of protein phosphatase 5 established by DFT calculations

artículo científico publicado en 2013

The current status of the NNRTI family of antiretrovirals used in the HAART regime against HIV infection

artículo científico publicado en 2008

The excision mechanism in reverse transcriptase: pyrophosphate leaving and fingers opening are uncoupled events with the analogues AZT and d4T.

artículo científico publicado en 2007

The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study

artículo científico publicado en 2012

The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions

artículo científico publicado en 2014

The inclusion of d-type Gaussian functions in the analytic method for the calculation of electrostatic molecular potentials. Interaction of a proton or a positive muon with carbon monoxide

The interaction of aluminum with catecholamine-based neurotransmitters: can the formation of these species be considered a potential risk factor for neurodegenerative diseases?

scientific article published on 01 May 2019

The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases

artículo científico publicado en 2017

The nature of trypsin-pancreatic trypsin inhibitor binding: free energy calculation of Tyr39-->Phe39 mutation in trypsin

artículo científico publicado en 1997

The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase

The search for a new model structure of beta-factor XIIa

artículo científico publicado en 2001

The search for the mechanism of the reaction catalyzed by farnesyltransferase

artículo científico publicado en 2009

Theoretical Studies on the Mode of Inhibition of Ribonucleotide Reductase by 2′-Substituted Substrate Analogues

Theoretical Study on the Inhibition of Ribonucleotide Reductase by 2‘-Mercapto-2‘-deoxyribonucleoside-5‘-diphosphates

artículo científico publicado en 2005

Theoretical insights into the catalytic mechanism of β-hexosaminidase

Theoretical insights into the mechanism for thiol/disulfide exchange

artículo científico publicado en 2004

Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes

artículo científico publicado en 2005

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

Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase

artículo científico publicado en 2013

Theoretical studies on the mechanism of inhibition of Ribonucleotide Reductase by (E)-2'-Fluoromethylene-2'-deoxycitidine-5'-diphosphate

artículo científico publicado en 2003

Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2'-azido-2'-deoxyribonucleoside 5'-diphosphates

artículo científico publicado en 2004

Theoretical study of the amino acid interactions in the binding region of the trypsin–pancreatic trypsin inhibitor complex

Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate.

artículo científico publicado en 2005

Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin

artículo científico publicado en 2006

Topological, hydrophobicity, and other descriptors on α-glucosidase inhibition: a QSAR study on xanthone derivatives

Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic

artículo científico publicado en 2022

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

artículo científico publicado en 2018

Tuning the affinity of catechols and salicylic acids towards Al(iii): characterization of Al–chelator interactions

scientific article published on 01 July 2018

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

scientific article published on 22 October 2018

Understanding ribonucleotide reductase inactivation by gemcitabine.

artículo científico publicado en 2007

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

Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2′- Deoxy-2′-methylenecytidine-5′-diphosphate

artículo científico publicado en 2010

Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase

scientific article published on 10 July 2018

Understanding the binding of procyanidins to pancreatic elastase by experimental and computational methods

artículo científico publicado en 2010

Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.

artículo científico publicado en 2017

Unraveling the Importance of Protein−Protein Interaction: Application of a Computational Alanine-Scanning Mutagenesis to the Study of the IgG1 Streptococcal Protein G (C2 Fragment) Complex

artículo científico publicado en 2006

Unraveling the enigmatic mechanism of L-asparaginase II with QM/QM calculations.

artículo científico publicado en 2013

Unraveling the mechanism of the farnesyltransferase enzyme

artículo científico publicado en 2004

Unravelling Hot Spots: a comprehensive computational mutagenesis study

Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations

Vascular endothelial growth factor (VEGF) inhibition--a critical review

artículo científico publicado en 2007

Vinylcatechin dimers are much better copigments for anthocyanins than catechin dimer procyanidin b3.

artículo científico publicado en 2010

Virtual Screening of Compound Libraries ⬇️

artículo científico publicado el 1 de enero de 2009

Virtual screening and QSAR study of some pyrrolidine derivatives as α-mannosidase inhibitors for binding feature analysis

artículo científico publicado en 2012

Virtual screening in drug design and development.

artículo científico publicado en 2010

Visualizing the Microscopic World

artículo científico publicado en 2017

Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems

artículo científico publicado en 2013

hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis

article

molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software

artículo científico publicado en 2018

α-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study.

artículo científico publicado en 2017

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