Rodrigo Antonio Faccioli

This project was idealized as a collaborative endeavor in the drug design area.

The current build allows s to perform Virtual Screening assays by employing the following software:

1. AutoDock Vina - vina.scripps.edu
2. MGLTools - mgltools.scripps.edu
3. Gromacs - www.gromacs.org
4. Apache Spark - spark.apache.org

The project was designed to be flexible and scalable, in order to adapt to a variety of different computational environments.

The main features… Mostrar más

This project was idealized as a collaborative endeavor in the drug design area.

The current build allows s to perform Virtual Screening assays by employing the following software:

1. AutoDock Vina - vina.scripps.edu
2. MGLTools - mgltools.scripps.edu
3. Gromacs - www.gromacs.org
4. Apache Spark - spark.apache.org

The project was designed to be flexible and scalable, in order to adapt to a variety of different computational environments.

The main features are described below:

1. Virtual Screening (using one or more receptors).
Analysis can be done by using both experimental (from the PDB database) and theoretical (from molecular dynamics simulation) data, thus providing a broader understanding about the selected compounds and receptors and generating more accurate results.

2. Big Data Analytics through Apache Spark.
Virtual Screening usually outputs a considerable amount of data, by using Spark this data can be analyzed more efficiently. Mostrar menos

The goal of this project is find potential inhibitors of dengue virus protease. Molecular Dynamics and Virtual Screening will be performed.

The goal of this project is development of web interface that enables the use of several algorithms for Biophysical molecular. Therefore, s have a standard interface to run programs. It is important in a multi-disciplinary area because s who are not skilled in computing can run programs that are necessary for them.

Aplicativo Android com o intuito de obter o dos usuários de transporte aéreo. Com esses s é possível alimentar um banco de dados que aplicando técnicas de datamining tornará possível mensurar a qualidade dos serviços aéreos.

This project is called ProtPred-GROMACS_Building_Conformation. The goal of this project is to generate protein 3D conformation. Based on primary sequence of protein is created 3D full-atom conformation randomly. The can chose the number of conformations. It is able to minimize these conformations using GROMACS algorithms. This project is developed in C language and it uses GNU Scientific Library (GSL) to generate random numbers. The integration with GROMACS is employed fork instead of… Mostrar más

This project is called ProtPred-GROMACS_Building_Conformation. The goal of this project is to generate protein 3D conformation. Based on primary sequence of protein is created 3D full-atom conformation randomly. The can chose the number of conformations. It is able to minimize these conformations using GROMACS algorithms. This project is developed in C language and it uses GNU Scientific Library (GSL) to generate random numbers. The integration with GROMACS is employed fork instead of system command to get more performance and control. Also, is used bash and python scripts to provide new functionalities. Mostrar menos

This project is called ProtPred-GROMACS (2PG). The goal of this project is to develop and to integrate optimization algorithms with molecular modeling software such as GROMACS. Here, it is developed in C language. The integration with GROMACS is automatically. Nowadays, this project has implemented: Evolutionary Algorithm Mono-Objective, Non-dominated Sorting Genetic Algorithm (NSGA-II), Monte Carlo Metropolis and Multicriterion Evaluation of Protein Structures (MEPS). Furthermore, It allows… Mostrar más

This project is called ProtPred-GROMACS (2PG). The goal of this project is to develop and to integrate optimization algorithms with molecular modeling software such as GROMACS. Here, it is developed in C language. The integration with GROMACS is automatically. Nowadays, this project has implemented: Evolutionary Algorithm Mono-Objective, Non-dominated Sorting Genetic Algorithm (NSGA-II), Monte Carlo Metropolis and Multicriterion Evaluation of Protein Structures (MEPS). Furthermore, It allows using Molecular Dynamics from GROMACS automatically. It was developed for applying problems in which not only is necessary sampling of search space looking for protein conformations with lowest energy but also ranking a set of protein conformations employing multi-criteria technique. Mostrar menos

Participation at CASP11 through 2PG branch.
The focus of 2PG branch was to generate models through molecular dynamics and to classify them based on dominance criteria.
First the proposed approach obtains models generated by the best public CASP-certified protein structure prediction servers and perform molecular dynamics simulations. After the simulations, the starting model and its last frame of molecular dynamics are ranked based on dominance criteria. We developed 2PG Sort-Dominance… Mostrar más

Participation at CASP11 through 2PG branch.
The focus of 2PG branch was to generate models through molecular dynamics and to classify them based on dominance criteria.
First the proposed approach obtains models generated by the best public CASP-certified protein structure prediction servers and perform molecular dynamics simulations. After the simulations, the starting model and its last frame of molecular dynamics are ranked based on dominance criteria. We developed 2PG Sort-Dominance software to rank the protein models. Mostrar menos

It is an experiment designed to compete and collaborate within Critical Assessment of protein Structure Prediction (CASP). My collaboration in this project was wfAll-MD-RFLB branch. All models submitted were ranked by based on dominance criteria. We developed 2PG Sort-Dominance software to rank the protein models. This project was an international cooperation for protein structure prediction area.

It is an experiment designed to compete and collaborate within Critical Assessment of protein Structure Prediction (CASP 10). My collaboration in this project was applying Replica Exchange Molecular Dynamics (REMD) into results from several methods published by . This project was an international cooperation for protein structure prediction area. The paper of this project was published at http://onlinelibrary.wiley.com/doi/10.1002/prot.24538/abstract.

The use of multi-objective evolutionary algorithms and molecular dynamics was investigated in Ab Initio protein structure prediction. It is a multidisciplinary area and requires softwares in which the can manipulate them without concern for all details about computational technical background because each area has their peculiarity. Therefore, a framework that integrate transparently these peculiarity for was built. This framework was written in C language. It has utilized in Linux… Mostrar más

The use of multi-objective evolutionary algorithms and molecular dynamics was investigated in Ab Initio protein structure prediction. It is a multidisciplinary area and requires softwares in which the can manipulate them without concern for all details about computational technical background because each area has their peculiarity. Therefore, a framework that integrate transparently these peculiarity for was built. This framework was written in C language. It has utilized in Linux environment. Besides, scripts which aid in the run of this framework were written in Python and bash Mostrar menos

Prometheus means PROtein-Protein Complexes by Macroscopic Electrostatic Theories and -Friendly Simulations. Starting with two protein structures (Fasta and/or PDB formats), the defines the experimental parameters (temperature, ionic strength and protein concentration) as inputs, and the Prometheus estimates the protein net charge and capacitance as a function of pH, electrostatic free energy derivatives and the second virial coefficients. The system is designed to be easily used by… Mostrar más

Prometheus means PROtein-Protein Complexes by Macroscopic Electrostatic Theories and -Friendly Simulations. Starting with two protein structures (Fasta and/or PDB formats), the defines the experimental parameters (temperature, ionic strength and protein concentration) as inputs, and the Prometheus estimates the protein net charge and capacitance as a function of pH, electrostatic free energy derivatives and the second virial coefficients. The system is designed to be easily used by s not familiar with computational techniques. In this project, I participated in the development of background that was implemented in Python and PostgreSQL. Also, the use of BioPython project was necessary to manipulate the biological information. Mostrar menos

An implementation of Non-dominated Sorting Genetic Algorithm II (NSGA-II) using Fuzzy logic was developed. This approach had the objective increase the sampling of search space to protein structure prediction. It was written in C language and Matlab. It ran in Windows environment.

I developed a software to search medical images on databases simultaneously. Doctor could see all images that wanted at his computer. This solution was based on medical images could be in different hospitals, clinics or others. Therefore, a doctor is able to analyze all images "just one by click". This software was written in Delphi with PostgreSQL database. It ran in Windows environment.