Marcelo C. R. Melo
I am currently a postdoctoral researcher in the Perelman School of Medicine at the University of Pennsylvania, advised by Professor Cesar de la Fuente. My work focuses on exploring the Gut-Brain axis from a computational biology perspective, combining machine learning with systems- and structural-biology approaches.
- Ph.D. in Biophysics (2019) – University of Illinois at Urbana-Champaign – USA
- M.S. in Biophysics (2013) – Federal University of Rio de Janeiro – Brazil
- B.S. in Biophysics (2011) – Federal University of Rio de Janeiro – Brazil
- Biological Systems
- Neuroactive Peptides
- Antimicrobial Peptides
- Cellular Metabolism
- Computational Methods Development
- Machine Learning
- Systems Biology
- Hybrid QM/MM Simulations
- Protein Folding
Current and Previous Research
Neuropeptides are a large class of structurally diverse small proteins that control neuronal function. Understanding how such peptides bind and activate their receptors is essential for the development and improvement of (ant)agonists of multiple pharmacologically relevant GPCR targets.
Hundreds of microbial species have been identified in our gut microbiome, however we still lack tools to precisely probe and engineer this community. Using systems biology tools to describe the interactions between microbial species is essential to develop predictive and quantitative models of our microbiome.
Hybrid QM/MM Simulations
The NAMD QM/MM interface extends existing NAMD features to the quantum mechanical level, presenting new features and possibilities. Investigations of processes occurring on a timescale usually not accessible by QM/MM methods can be performed by combining enhanced sampling and free energy calculation method already present in NAMD. Taking advantage of an easy-to-use Tcl based interface and capabilities integrated from VMD, this interface has the ability to execute multiple QM regions in parallel, thorough independent executions of your choice of quantum chemistry code.
Protein Folding and Enhanced Sampling
GSAFold applies the Generalized Simulated Annealing (GSA) algorithm for ab-initio structure prediction of small proteins and intrinsically disordered regions. This new package combines a precise implementation of GSA with the broadly used NAMD Molecular Dynamics software to carry out energy calculations, allowing the user to select different force fields and parameterizations.
- Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories ; Melo MCR, Bernardi RC, de la Fuente-Nunez C, Luthey-Schulten Z ; In Press, 2020
- Scalable molecular dynamics on CPU and GPU architectures with NAMD ; James C Phillips, David J Hardy, Julio DC Maia, John E Stone, João V Ribeiro, Rafael C Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo CR Melo, Brian K Radak, Robert D Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V Kalé, Klaus Schulten, Christophe Chipot, Emad Tajkhorshid ; The Journal of Chemical Physics, 2020
- Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly ; Chen* CH, Melo* MCR, Berglund N, Khan A, de la Fuente-Nunez C, Ulmschneider JP, Ulmschneider MB; Current Opinion in Structural Biology, 2020
- Kinetic Modeling of the Genetic Information Processes in a Minimal Cell ; Thornburg ZR, Melo MCR, Bianchi D, Brier TA, Crotty C, Breuer M, Smith HO, Hutchison CA III, Glass JI and Luthey-Schulten Z ; Frontiers in Molecular Biosciences, 2019
- NAMD goes quantum: An integrative suite for hybrid simulations ; Melo* MCR, Bernardi* RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GD, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z ; Nature Methods, 2018
- Direction Matters: Monovalent Streptavidin/Biotin Complex under Load ; Sedlak* SM, Schendel* LC, Melo MCR, Pippig DA, Luthey-Schulten Z, Gaub HE, Bernardi RC ; Nano Letters, 2018
- Population FBA predicts metabolic phenotypes in yeast ; Labhsetwar* P, Melo* MCR, Cole* JA, Luthey-Schulten Z; PLoS Computational Biology, 2017
- Enhanced sampling techniques in molecular dynamics simulations of biological systems; Bernardi RC, Melo MCR, Schulten K; Biochimica et Biophysica Acta (BBA), 2015
- GSAFold: A new application of GSA to protein structure prediction; Melo MCR, Bernardi RC, Fernandes TVA, Pascutti PG; Proteins: Structure, Function, and Bioinformatics, 2012