List of works - Ricardo L Mancera

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information.

scientific article

A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein

scientific article published in July 2003

A new method for estimating the importance of hydrophobic groups in the binding site of a protein

scientific article published on 01 February 2005

Adsorption and Unfolding of Lysozyme at a Polarized Aqueous-Organic Liquid Interface.

scientific article published on 7 March 2016

Assessment of multiple binding modes in ligand-protein docking.

scientific article published in June 2004

Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps).

scientific article

AutoMap: a tool for analyzing protein-ligand recognition using multiple ligand binding modes.

scientific article published on 8 January 2013

Can current force fields reproduce ring puckering in 2-O-sulfo-alpha-L-iduronic acid? A molecular dynamics simulation study

scientific article

Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies

scientific article published on 25 August 2018

Characterization of Protein-Facilitated Ion-Transfer Mechanism at a Polarized Aqueous/Organic Interface

scientific article published on 19 August 2019

Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials

scientific article published on 10 February 2014

Comparative analysis of the surface interaction properties of the binding sites of CDK2, CDK4, and ERK2.

scientific article

Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.

scientific article published in October 2004

Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-D-glucuronidase (heparanase).

scientific article

Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase.

scientific article published on 15 May 2017

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

scientific article

Development and application of site mapping methods for the design of glycosaminoglycans

scientific article published on 23 May 2014

Does Sucrose Change Its Mechanism of Stabilization of Lipid Bilayers during Desiccation? Influences of Hydration and Concentration

scientific article published on 18 November 2019

Enhanced transdermal peptide delivery and stability by lipid conjugation: epidermal permeation, stereoselectivity and mechanistic insights

scientific article published on 21 May 2014

Erdheim-Chester disease associated with a novel, complex BRAF p.Thr599_Val600delinsArgGlu mutation

scientific article

Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex.

scientific article

Free energy calculations of glycosaminoglycan-protein interactions

scientific article published on 30 July 2009

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein.

scientific article

Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping

scientific article

Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells.

scientific article

Heparin/heparan sulphate-based drugs ⬇️

scientific article published on October 23, 2010

Hydrogen bond disruption in DNA base pairs from (14)C transmutation

scientific article published on 25 August 2014

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

scientific article published in May 2005

Influence of Bilayer Size and Number in Multi-Bilayer DOPC Simulations at Full and Low Hydration

scientific article published on 25 January 2019

Inhibitors of Xanthine Oxidase: Scaffold Diversity and Structure-Based Drug Design

scientific article published on 05 March 2019

Ligand-protein docking using a quantum stochastic tunneling optimization method.

scientific article published in April 2004

Ligand-protein docking with water molecules

scientific article published on 23 January 2008

Molecular Dynamics Simulation of Tau Peptides for the Investigation of Conformational Changes Induced by Specific Phosphorylation Patterns.

scientific article published on January 2017

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

scientific article published on 21 June 2018

Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment

scientific article published on 24 March 2014

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

scientific article published on 07 February 2011

Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field

scientific article published on 25 June 2018

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein.

scientific article published on 15 April 2008

Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes.

scientific article

Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer

scientific article published on 21 May 2013

Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers

scientific article published on June 2014

Monitoring of oxidative status in three native Australian species during cold acclimation and cryopreservation

scientific article

Myrtaceae in Australia: Use of Cryobiotechnologies for the Conservation of a Significant Plant Family under Threat

scientific article published on 09 April 2022

New anti-tuberculosis drugs with novel mechanisms of action.

scientific article published on January 2008

New arylated benzo[h]quinolines induce anti-cancer activity by oxidative stress-mediated DNA damage.

scientific article published on 06 December 2016

Novel Structural Features of CDK Inhibition Revealed by an ab Initio Computational Method Combined with Dynamic Simulations

scientific article published on 01 August 2006

Optimization of protein-protein docking for predicting Fc-protein interactions.

scientific article published on 22 July 2016

Optimization of surface plasmon resonance experiments: Case of high mobility group box 1 (HMGB1) interactions.

scientific article

Prediction of heparin binding sites in bone morphogenetic proteins (BMPs)

scientific article published on 21 July 2012

Quantitative structure-activity relationships of competitive inhibitors of phosphoenolpyruvate carboxylase

scientific article published on 01 March 1995

Revisiting the Interaction of Melittin with Phospholipid Bilayers: The Effects of Concentration and Ionic Strength

scientific article published on 23 January 2020

Role of the cell membrane interface in modulating production and uptake of Alzheimer's beta amyloid protein.

scientific article published on 20 March 2018

Secondary Structural Changes in Proteins as a Result of Electroadsorption at Aqueous-Organogel Interfaces

scientific article published on 18 April 2019

Seed storage behaviour of tropical members of the aquatic basal angiosperm genus L. (Nymphaeaceae)

scientific article published on 10 May 2019

Studies of the benzopyran class of selective COX-2 inhibitors using 3D-QSAR and molecular docking.

scientific article published on 18 August 2017

The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

scientific article

The effect of physicochemical factors on the self-association of HMGB1: A surface plasmon resonance study.

scientific article published on 28 July 2016

The effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations

scientific article published on 13 March 2013

The self-association of HMGB1 and its possible role in the binding to DNA and cell membrane receptors.

scientific article published on 27 December 2016

The structure of glycosaminoglycans and their interactions with proteins.

scientific article published on December 2008

The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides

scientific article published on 16 October 2019

Thermodynamics of the hydration of non-polar substances

scientific article published on 01 January 1998

Towards an understanding of the molecular basis of hydrophobicity

scientific article published on 01 August 1996

Understanding Insulin Endocrinology in Decapod Crustacea: Molecular Modelling Characterization of an Insulin-Binding Protein and Insulin-Like Peptides in the Eastern Spiny Lobster, Sagmariasus verreauxi.

scientific article published on 23 August 2017

Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system

scientific article published on 09 August 2016

List of works by Ricardo L Mancera

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information.

A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein

A new method for estimating the importance of hydrophobic groups in the binding site of a protein

Adsorption and Unfolding of Lysozyme at a Polarized Aqueous-Organic Liquid Interface.

Assessment of multiple binding modes in ligand-protein docking.

Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps).

AutoMap: a tool for analyzing protein-ligand recognition using multiple ligand binding modes.

Can current force fields reproduce ring puckering in 2-O-sulfo-alpha-L-iduronic acid? A molecular dynamics simulation study

Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies

Characterization of Protein-Facilitated Ion-Transfer Mechanism at a Polarized Aqueous/Organic Interface

Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials

Comparative analysis of the surface interaction properties of the binding sites of CDK2, CDK4, and ERK2.

Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.

Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-D-glucuronidase (heparanase).

Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase.

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

Development and application of site mapping methods for the design of glycosaminoglycans

Does Sucrose Change Its Mechanism of Stabilization of Lipid Bilayers during Desiccation? Influences of Hydration and Concentration

Enhanced transdermal peptide delivery and stability by lipid conjugation: epidermal permeation, stereoselectivity and mechanistic insights

Erdheim-Chester disease associated with a novel, complex BRAF p.Thr599_Val600delinsArgGlu mutation

Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex.

Free energy calculations of glycosaminoglycan-protein interactions

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein.

Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping

Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells.

Heparin/heparan sulphate-based drugs ⬇️

Hydrogen bond disruption in DNA base pairs from (14)C transmutation

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

Influence of Bilayer Size and Number in Multi-Bilayer DOPC Simulations at Full and Low Hydration

Inhibitors of Xanthine Oxidase: Scaffold Diversity and Structure-Based Drug Design

Ligand-protein docking using a quantum stochastic tunneling optimization method.

Ligand-protein docking with water molecules

Molecular Dynamics Simulation of Tau Peptides for the Investigation of Conformational Changes Induced by Specific Phosphorylation Patterns.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein.

Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes.

Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer

Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers

Monitoring of oxidative status in three native Australian species during cold acclimation and cryopreservation

Myrtaceae in Australia: Use of Cryobiotechnologies for the Conservation of a Significant Plant Family under Threat

New anti-tuberculosis drugs with novel mechanisms of action.

New arylated benzo[h]quinolines induce anti-cancer activity by oxidative stress-mediated DNA damage.

Novel Structural Features of CDK Inhibition Revealed by an ab Initio Computational Method Combined with Dynamic Simulations

Optimization of protein-protein docking for predicting Fc-protein interactions.

Optimization of surface plasmon resonance experiments: Case of high mobility group box 1 (HMGB1) interactions.

Prediction of heparin binding sites in bone morphogenetic proteins (BMPs)

Quantitative structure-activity relationships of competitive inhibitors of phosphoenolpyruvate carboxylase

Revisiting the Interaction of Melittin with Phospholipid Bilayers: The Effects of Concentration and Ionic Strength

Role of the cell membrane interface in modulating production and uptake of Alzheimer's beta amyloid protein.

Secondary Structural Changes in Proteins as a Result of Electroadsorption at Aqueous-Organogel Interfaces

Seed storage behaviour of tropical members of the aquatic basal angiosperm genus L. (Nymphaeaceae)

Studies of the benzopyran class of selective COX-2 inhibitors using 3D-QSAR and molecular docking.

The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

The effect of physicochemical factors on the self-association of HMGB1: A surface plasmon resonance study.

The effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations

The self-association of HMGB1 and its possible role in the binding to DNA and cell membrane receptors.

The structure of glycosaminoglycans and their interactions with proteins.

The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides

Thermodynamics of the hydration of non-polar substances

Towards an understanding of the molecular basis of hydrophobicity

Understanding Insulin Endocrinology in Decapod Crustacea: Molecular Modelling Characterization of an Insulin-Binding Protein and Insulin-Like Peptides in the Eastern Spiny Lobster, Sagmariasus verreauxi.

Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system