From my undergraduate to my current position as Postdoctoral Research, I had the opportunity to combine biology/biochemistry with computer science. My research focus is in improving the usability of computational chemistry tools to overcome the initial learning curve barrier and computational technical difficulties (e.g. use of scripting languages), hindering the general use of these tools.
During my PhD in Science Faculty of Porto University, I had the opportunity to develop different VMD third-party tools (plugins) to assist the user in the drug development working on a Computational Chemistry Lab. These tools were based in a world wide used software, such as VMD, NAMD, AMBER, AutoDock and AutoDock Vina.
As the main developer of QwikMD, my most recent project, my main purpose is to develop a tool to assist experimentalists and any novice to MD to overcome the initial learning curve barrier of MD simulation software. QwikMD streamlines common processes, such as the generation of the structure and NAMD configuration files, so the user can focus on the scientific question. Far from being a black box, QwikMD gives the user full access to the options necessary to adjust QwikMD work-flow to the specificity of each project. Even more advanced users can benefit from using QwikMD as the "Advance" mode offers more complex functionalities such as membrane insertion, text mode NAMD configuration edition, creation and edition of user-defined MD protocols.
Home Department: Beckman Institute for Advanced Science and Technology.
Office Address: Beckman Institute, Room 3165.
Office Phone: (217) 300-0380
Email Address: firstname.lastname@example.org
- PhD in Chemistry (2014) - - Faculty of Sciences, University of Porto - Portugal
Advisor: Dra. Maria João Ramos
- Diploma Degree in Bioinformatics (2009) - - Biotechnology Superior School, Universidade Católica Portuguesa - Portugal
Advisor: Dra. Célia Manaia
- Second-generation Biofuel
- Protein-Protein interactions
- Molecular Biology
- Molecular Docking
- Molecular Dynamics
- Molecular Visualization
- Molecular Structure
QwikMD - Gateway to Easy Simulation
To assist experimentalists and any novice to MD to overcome the initial learning currve barrier of MD simulation software, we developed QwikMD, a user interface that connects the widely employed and user-friendly molecular graphics program VMD to the widely adopted MD program NAMD.
By enabling easy control of every step, QwikMD, meets even the needs of experts in the field, increasing the efficiency and quality of their work.
Easy Setup of MD Simulations
Changes in Protonation
Protocols for MD and SMD
Live View Simulations
Integrated Basic Analysis
Info Buttons to Guide Novices
Available on Amazon Cloud
Full log Capabilities
My previous work was dedicated to the development of VMD plugins aiming to aid the user in the use commonly applied computational chemistry techniques, such as Molecular Docking (vsLab), Molecular Volume and Surface calculation(VolArea), Computational Alanine Scanning Mutagenesis(compASM) and to locate chemical motifs in protein structures(Chem-Path-Tracker)
- Making Classical and Hybrid (QM/MM) Molecular Dynamics Easy and Fast with QwikMD; JV Ribeiro,RC Bernardi, T Rudack, K Schulten, Biophysical Journal. 2017
- QwikMD Integrative Molecular Dynamics Toolkit for Novices and Experts; JV Ribeiro, RC Bernardi, T Rudack, JE Stone ,JC Phillips,PL Freddolino, K Schulten; Scientific Reports. 2016
- Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing; JE Stone, M Sener, KL Vandivort, A Barragan, A Singharoy, I Teo, JV Ribeiro, B Isralewitz, B Liu, BC Goh, JC Phillips, C MacGregor-Chatwin, MP Johnson, LF Kourkoutis, CN Hunter, K Schulten, Parallel Computing. 2016
- Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists; JV Ribeiro,RC Bernardi, T Rudack, K Schulten, Biophysical Journal. 2016
- Chem-Path-Tracker: An automated tool to analyze chemical motifs in molecular structures; JV Ribeiro, NMFSA Cerqueira PA Fernandes and MJ Ramos, Chem Biol Drug Des. 2014 (Cover)
- Volarea - A bioinformatics tool to calculate the surface area and the volume of molecular systems;JV Ribeiro, JAC Tamames, NMFSA Cerqueira PA Fernandes and MJ Ramos, Chem Biol Drug Des. 2013
- CompASM: an Amber-VMD alanine scanning mutagenesis plug-in; JV Ribeiro, NMFSA Cerqueira, I Moreina, PA Fernandes and MJ Ramos, Theor Chem Acc 2012
- VsLab-An implementation for virtual high-throughput screening using AutoDock and VMD; NMFSA Cerqueira, J Ribeiro, PA Fernandes and MJ Ramos, Quantum Chem 2011