List of works by 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.

scientific article published on 20 March 2018

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

scientific article published in December 2016

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

scientific article published on 11 January 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

scientific article published in December 2003

A new device for treatment of persistent otitis media with effusion

scientific article published on 22 October 2013

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

scientific article published on 9 December 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.

scientific article published on 21 February 2018

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

scientific article published in July 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

scientific article published on 07 November 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

scientific article (publication date: 15 November 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.

scientific article published in November 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

scientific article published on 27 March 2012

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

article

Anandamide targets aromatase: A breakthrough on human decidualization

scientific article published on 24 August 2019

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

scientific article published in November 2008

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

scientific article published in September 2016

Are hot-spots occluded from water?

scientific article published on 5 February 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

scientific article published on 03 September 2020

Atomic-Level Rational Drug Design

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

scientific article published in August 2010

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

scientific article

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

scientific article published on 23 May 2014

Backbone Importance for Protein−Protein Binding†

scientific article published on 01 May 2007

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

scientific article published on 05 June 2019

Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds

scientific article published on 08 July 2010

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

scientific article published on 01 November 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

scientific article

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

scientific article published in June 2006

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

scientific article

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

scientific article

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

scientific article published in May 2000

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

scientific article published on 7 June 2014

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

scientific article

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

scientific article

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

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

scientific article published on 01 February 2019

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

scientific article

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

scientific article published on 09 November 2012

Cholesterol Biosynthesis: A Mechanistic Overview.

scientific article published on 7 September 2016

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

scientific article published on 6 June 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.

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

scientific article

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

scientific article

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI.

scientific article published on 25 February 2013

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

Computational Enzymatic Catalysis

article published in 2008

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

scientific article published on 29 March 2011

Computational alanine scanning mutagenesis--an improved methodological approach

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

scientific article published on 27 July 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

scientific article published on 06 August 2012

Computational insight into anti-mutagenic properties of CYP1A flavonoid ligands

scientific article published in July 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

scientific article published in September 2003

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

scientific article

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

scientific article published in August 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)

scientific article published in 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

scientific article published on June 2004

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

scientific article

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.

scientific article published in June 2006

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

scientific article published on 2 December 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.

scientific article

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

scientific article published in 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.

scientific article published on January 2009

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

scientific article

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

scientific article published on 27 March 2014

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

scientific article published in April 2014

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

scientific article

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

scientific article published in 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

scientific article published on 01 June 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

scientific article published in December 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.

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?

Foreword

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

scientific article published on January 2014

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

Gathering computational genomics and proteomics to unravel adaptive evolution

scientific article

General performance of density functionals

scientific article published on 25 August 2007

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

scientific article

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

scientific article published in February 2010

Glutathione transferase A1-1: catalytic role of water

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

scientific article published in October 2010

Glutathione transferase: new model for glutathione activation

scientific article

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

scientific article

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

scientific article published on 18 August 2016

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

scientific article published on 22 February 2007

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

scientific article published on September 2007

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

scientific article published on January 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.

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

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

scientific article published on November 1997

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

scientific article published on 9 October 2017

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

scientific article published on 27 November 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

scientific article published in April 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

scientific article published on 11 April 2016

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

scientific article published on 21 December 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

scientific article published on 28 April 2014

Ligand based analysis on HMG-CoA reductase inhibitors

article

MADAMM: a multistaged docking with an automated molecular modeling protocol

scientific article

Mammalian cytosolic glutathione transferases

scientific article published on August 2008

Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine

scientific article

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 fromShewanella frigidimarina: A Theoretical Study

scientific article published on 01 June 2006

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

scientific article published in February 2008

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

scientific article published on 12 November 2017

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

scientific article published on 16 March 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

scientific article published on 30 May 2017

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

scientific article published in November 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

scientific article published on 21 May 2010

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

Mitochondrial introgressions into the nuclear genome of the domestic cat.

scientific article published on 28 July 2007

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

scientific article published on June 1, 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.

scientific article published on 6 December 2017

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

scientific article

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

scientific article published on 6 January 2018

Molecular Dynamics Analysis of FAAH Complexed with Anandamide

scientific article published in 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.

scientific article

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

scientific article published on 19 September 2008

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

scientific article

Molecular dynamics studies on both bound and unbound renin protease.

scientific article

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

scientific article

Molecular interactions between human cytochrome P450 1A2 and flavone derivatives.

scientific article published in July 2006

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

scientific article published on 12 October 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

scientific article published in 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

scientific article published on 12 December 2016

New designs for MRI contrast agents.

scientific article published in July 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

scientific article (publication date: August 2003)

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

scientific article published on September 2004

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

scientific article

PLP undergoes conformational changes during the course of an enzymatic reaction

scientific article

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

article

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

scientific article

Parameters for molecular dynamics simulations of iron-sulfur proteins

scientific article

Parametrization of Molybdenum Cofactors for the AMBER Force Field

scientific article published on 16 April 2018

Parametrization of Synthetic Amino Acids

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

scientific article published on 28 October 2015

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

scientific article published on August 2014

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

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

scientific article published on 08 April 2013

Preface

Properties that rank protein:protein docking poses with high accuracy

scientific article published on 01 August 2018

Protein-ligand docking: current status and future challenges

scientific article published on October 2006

Protein-protein docking dealing with the unknown

scientific article published on January 2010

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

Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation

scientific article

Pyruvate Formate Lyase: A New Perspective

article published in 2003

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

scientific article published on February 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

scientific article published on 11 November 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

scientific article published on 01 November 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

scientific article published on 01 March 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.

scientific article

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

scientific article published in October 2014

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

scientific article published on 25 May 2016

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

scientific article

Receptor-based virtual screening protocol for drug discovery.

scientific article published on June 2015

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

scientific article

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

scientific article published on 7 April 2017

Ribonucleotide Reductase – Computational Studies

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

scientific article

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

scientific article published on January 2007

Ribonucleotide reductase: a mechanistic portrait of substrate analogues inhibitors.

scientific article published on January 2010

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

scientific article

Similarities and differences in the thioredoxin superfamily

scientific article

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

article

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

scientific article published on 04 May 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

article

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).

scientific article published on 15 October 2013

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 4 December 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

scientific article published on 5 July 2013

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

scientific article published on 4 October 2008

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

scientific article

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.

scientific article published on July 2012

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

scientific article

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

scientific article published on 12 June 2015

Synthesis and structural characterization of two diasteroisomers of vinylcatechin dimers

scientific article published in November 2009

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

scientific article

The Catalytic Mechanism of Carboxylesterases: A Computational Study

scientific article published on 04 September 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.

scientific article published on 18 March 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.

scientific article published on 14 June 2017

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

scientific article

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

scientific article

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

scientific article (publication date: 4 March 2008)

The barriers to internal rotation for muonic-substituted ethyl radicals

The carboxylate shift in zinc enzymes: a computational study.

scientific article published in February 2007

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

scientific article published on 13 July 2012

The catalytic mechanism of protein phosphatase 5 established by DFT calculations

scientific article published on 6 September 2013

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

scientific article published on January 2008

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

scientific article published on 22 September 2007

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

scientific article published on 12 June 2012

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

scientific article

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

scientific article published on 28 April 2017

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

scientific article published on 01 November 1997

The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase

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

scientific article published on 01 April 2001

The search for the mechanism of the reaction catalyzed by farnesyltransferase.

scientific article published in January 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

scientific article published in 2005

Theoretical insights into the catalytic mechanism of β-hexosaminidase

Theoretical insights into the mechanism for thiol/disulfide exchange

scientific article published in January 2004

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

scientific article published in July 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

scientific article published on 11 August 2013

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

scientific article

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

scientific article published in January 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.

scientific article published in May 2005

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

scientific article published in March 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

scientific article published on 12 May 2022

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

scientific article

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.

scientific article

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

scientific article published on 01 September 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

scientific article published in June 2010

Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.

scientific article published on 3 January 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

scientific article published on 01 June 2006

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

scientific article published on 6 May 2013

Unraveling the mechanism of the farnesyltransferase enzyme

scientific article

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

scientific article published on March 2007

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

scientific article published in March 2010

Virtual Screening of Compound Libraries ⬇️

scientific article published on January 1, 2009

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

scientific article published on 26 October 2012

Virtual screening in drug design and development.

scientific article

Visualizing the Microscopic World

scientific article published on 9 August 2017

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

scientific article published on 25 October 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

scientific article published on 21 February 2018

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

scientific article published in December 2017

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