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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
BASH scripting para principiantes
Published:
Tutorial de BASH scripting para alunos de iniciação científica e pós-graduação
O quê devo instalar na minha estação de trabalho?
Published:
Instalação do Miniconda e outros programas importantes para simulações moleculares
Dinâmica molecular de proteína e ligante em solvente
Published:
Tutorial de dinâmica molecular para avaliar a estabilidade da pose de um ligante dentro do sítio ativo de uma proteína.
Preparação para docking com o DOCK 6
Published:
Tutorial de preparação para docking de ligante em proteína
publications
Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database
Published in Journal of Chemical & Engineering Data, 2017
Minireview about solvation free energy calculations and update of FreeSolv, a experimental and computational free energy of solvation database.
Recommended citation: G. Duarte Ramos Matos, et al. (2017). "Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database." J. Chem. Eng. Data. 62 (5) 1559-1569. http://gduarter.github.io/files/2017-FreeSolv.pdf
Molecular dynamics simulations of montmorillonite reinforcing amylose plasticized by Brazilian Cerrado oils: polymer-clay nanocomposite
Published in MRS Communications, 2018
Study aimed at understanding the dynamics of fatty acids found in vegetable oils in montmorillonite as a means of understanding polymer-clay nanocomposites.
Recommended citation: F. A. R. Silva, M. J. A. Sales, M. Ghoul, L. Chebil, G. Duarte Ramos Matos, E. R. Maia (2018). "Molecular dynamics simulations of montmorillonite reinforcing amylose plasticized by Brazilian Cerrado oils: polymer-clay nanocomposite." MRS Communications. 8, 266-274. http://gduarter.github.io/files/2018-MD_montmorillonite.pdf
Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages
Published in Journal of Chemical Theory and Computation, 2018
Description of relative alchemical free energy calculations and their reproducibility accross different software.
Recommended citation: Hannes Loeffler et al. (2018). "Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages." J. Chem. Theory Comput.. 14(11) 5567-5582. http://gduarter.github.io/files/2018-Reproducibility.pdf
Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules
Published in F1000Research, 2019
The solubility of molecular crystals is a challenging physical property to predict. In this paper we discuss the efforts of estimating the solubility of molecular crystals using free energy calculations.
Recommended citation: G. Duarte Ramos Matos, D. L. Mobley (2019). "Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules." F1000Research. 7:686. http://gduarter.github.io/files/2019-Solubility.pdf
Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules
Published in Journal of Chemical Theory and Computation, 2019
Infinite dilution activity coefficients (IDACs) express the degree of non-ideality a solution has in infinitely dilute conditions and are important parameters for chemical plant design. This paper uses solvation free energy calculations to estimate IDACs and show that they are good alternatives to solvation free energies as validation tools in Computational Chemistry.
Recommended citation: G. Duarte Ramos Matos et al. (2019). "Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development." J. Chem. Theory Comput.. 15 (5), 3066-3074. http://gduarter.github.io/files/2019-IDAC.pdf
Rational Design and Multicomponent Synthesis of Lipid–Peptoid Nanocomposites towards a Customized Drug Delivery System Assembly
Published in Molecules, 2023
we describe a fundamental model proposal for the future development of lipid–peptoid-based customized drug delivery systems. This proposal was built based on the synthesis of a wide variety of peptoids with structural diversity via the Ugi reaction, followed by nanoformulations through the emulsification–evaporation process and molecular dynamics simulations.
Recommended citation: T. P. F. Rosalba, G. Duarte Ramos Matos, C. E. M. Salvador, C. K. Z. Andrade (2023). "Rational Design and Multicomponent Synthesis of Lipid–Peptoid Nanocomposites towards a Customized Drug Delivery System Assembly." Molecules. 28, 5725. http://gduarter.github.io/files/2023-Nano.pdf
Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit
Published in Journal of Chemical Information and Modeling, 2023
The primary objective of the present study is three-fold: (1) implement and validate a robust interface enabling DOCK6 to communicate with the open-source cheminformatics package RDKit,22 (2) confirm that the use of DOCK_D3N protocols leads to ligand ensembles that conform to the desired target values for the descriptors under different conditions and environments, and (3) examine ligand growth behavior using very narrow ranges for descriptors derived from clinically relevant compounds.
Recommended citation: G. Duarte Ramos Matos, S. Pak, R. C. Rizzo (2023). "Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit." J. Chem. Inf. Model.. 63, 5803-5822. http://gduarter.github.io/files/2023-D3N.pdf
Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports
Published in Organic & Biomolecular Chemistry, 2024
In this study, we present our findings concerning solvent effects on Biginelli-like MCRs, the mechanistic pathways of these transformations, and associated side reactions. We also advocate for a comprehensive correction of the vast existing literature on this topic.
Recommended citation: P. S. Beck, A. G. Leitão, Y. B. Santana, J. R. Correa, C. V. S. Rodrigues, D. F. S. Machado, G. Duarte Ramos Matos, L. M. Ramos, C. C. Gatto, S. C. C. Oliveira, C. K. Z. Andrade, B. A. D. Neto (2024). "Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports." Org. Biomol. Chem.. 22, 3630. http://gduarter.github.io/files/2024-Biginelli.pdf
teaching
Honors and Majors General Chemistry Lab A (CHEM H2LA/M2LA)
Undergraduate course, University of California Irvine, Department of Chemistry, 2013
Training and experience in fundamental and analytical laboratory techniques through experiments related to lecture topics in general Chemistry with applications to life sciences, physical sciences, and engineering. Atomic structure; general properties of the elements; covalent, ionic, and metallic bonding; mass relationships.
Honors and Majors General Chemistry Lab B (CHEM H2LB/M2LB)
Undergraduate course, University of California Irvine, Department of Chemistry, 2014
Training and experience in fundamental and analytical laboratory techniques through experiments related to lecture topics in general chemistry with applications to life sciences, physical sciences, and engineering. Properties of gases, liquids, solids; intermolecular forces; changes of state; properties of solutions; stoichiometry; thermochemistry; and thermodynamics.
Molecular Pharmacology II (PHARMSCI 170B)
Undergraduate course, University of California Irvine, Department of Pharmaceutical Sciences, 2015
Introductory survey covering the molecular mechanisms of drugs that target the nervous system, such as anxiolytics, antidepressants, antipsychotics, hypnotics, muscle relaxants, and recreational drugs; drugs related to the immune system, including antibiotics, antihistamines, and immunosuppressants; drugs used to treat cancer.
Introduction to Computational Organic Chemistry (CHEM 138)
Undergraduate course, University of California Irvine, Department of Chemistry, 2016
An introduction to the use of computational chemistry to investigate reaction mechanisms, to calculate structures, and to predict properties of molecules. Students have the opportunity to perform calculations employing computational methods which are widely used in various fields of chemistry.
General Chemistry Lab C (CHEM 1LC)
Undergraduate course, University of California Irvine, Department of Chemistry, 2018
Training and experience in fundamental and analytical laboratory techniques through experiments related to lecture topics in general Chemistry with applications to life sciences, physical sciences, and engineering. Atomic structure; general properties of the elements; covalent, ionic, and metallic bonding; mass relationships; properties of gases, liquids, solids; intermolecular forces; changes of state; properties of solutions; stoichiometry; thermochemistry; and thermodynamics.
Molecular Modeling of Biological Molecules (AMS 536)
Graduate course, Stony Brook University, Department of Applied Mathematics and Statistics, 2020
This computer-based lab course is designed for students who wish to gain hands an experience modeling biological molecules at the atomic level. In conjunction with individual interests, Molecular Mechanics, Molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages can be used to study relevant biological systems (s). Projects will include setup, execution, and analysis. Course participants will give literature presentations relevant to the simulations being performed and a final project report will be required. Familiarity with Unix (Linux) is desirable but not mandatory.
Introduction to Computational Structural Biology and Drug Design (AMS 535)
Graduate course, Stony Brook University, Department of Applied Mathematics and Statistics, 2020
This course provides an introduction to Computational Structural Biology with application to Drug Design. Methods and applications that use computation to model biological systems involved in human disease will be emphasized. The course aims to foster collaborative learning and will consist of presentations by the instructor, guest lecturers, and by course participants with the goal of summarizing key, methods, topics, and papers relevant to Computational Structural Biology. Grades are based on the quality of the presentations, participation in class discussion, attendance, quizzes, and a final exam.
Chemical Thermodynamics (IQD 0101)
Undergraduate course, Universidade de Brasília, Instituto de Química, 2022
Upper-division Physical-Chemistry course intending to deepen the understanding of chemical phenomena by making connections between classical thermodynamics and the microscopic world. Focus on the study of equilibrium states and their stability.
Introduction to Modern Chemistry (IQD 0191)
Undergraduate course, Universidade de Brasília, Instituto de Química, 2023
Lower-division Physical-Chemistry course intending to introduce the students to important concepts of Quantum Mechanics that are frequently used in Chemistry.