I'm a experienced researcher with a diverse background in computational biology, molecular modeling, and high-performance computing (HPC). I've mentored several graduate studends while teaching within the fields of Biochemistry, Bioinformatics, Biophysics, and Computational Chemistry. I'm an expert in Molecular Modeling & Dynamics for protein engineering and drug discovery. I'm passionate about enabling my peers to do great science.

I contribute significantly to various research projects, including the development of the Visual Molecular Dynamics (VMD) software, conducting Molecular Dynamics Simulations (NAMD), and contributing to the CyberShuttle project, aimed at accelerating scientific discovery.

Home Department: Physics Department at Auburn University

Office Address: 380 Duncan Dr, Auburn, AL 36832

Office Phone: +1 334 844-4264

Email Address:


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Research Interests

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CyberInfraStructure and Databases

  • Marru, S; Pierce, M; Plale, B; Pamidighantam, S; Wannipurage, D; Christie, M; Ranawaka, I; Abeysinghe, E; Quick, R; Tajkhorshid, E; Koric, S; Basney, J; Spivak M; Isralewitz B; Bernardi R; Gomes D; Krishnan G; Bazhenov M; Smallen S; Majumdar S; Arkhipov A, Dai K; Liu, Xiao-Ping.
    Cybershuttle: An end-to-end Cyberinfrastructure Continuum to accelerate Discovery in Science and Engineering.
    PERC23 - Practice & Experience in Advanced Research Computing (2023). doi: 10.1145/3569951.3593602
  • Gomes D.E.B; Galentino K; Sisquellas M; Monari L; Bouysset C; Cecchini M.
    ChemFlow─From 2D Chemical Libraries to Protein–Ligand Binding Free Energies.
    Journal of Chemical Information and Modeling (2023). doi: 10.1021/acs.jcim.2c00919
  • Naranjo-Feliciano D, Izquierdo-Alvarez L, Calero-Ramos R, Hernández-Alvarez L, Bouza-Figueroa J, Gomes DEB; Valiente PA, Calvet HAC, Pacutti PG.
    A molecular docking integrated platform for virtual screening of bioactive compounds.
    Biotecnologia Aplicada. (2021); 38(3):3211-3217.
  • Cerdan AH, Sisquellas M, Pereira G, Gomes DEB, Changeux JP, Cecchini M. 2020.
    The Glycine Receptor Allosteric Ligands Library (GRALL).
    Bioinformatics (2020) doi:10.1093/bioinformatics/btaa170
  • Silva, Alan, Osthoff, Carla, Oliveira, Cristiane, Gomes, D.E.B., Hill, E., Dardenne, L. E., Barros, P. M., Loureiro , P. A. A .G. L., Novaes, R, Pascutti, P G.
    The BioPAUÁ Project: A Portal for Molecular Dynamics Using Grid Environment.
    Lecture Notes in Computer Science (2005). v.3594, p.214 - 217.

Machine Learning and Artificial Intelligence

  • Melo MC; Gomes D.E.B.; Bernardi R.C.
    Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections.
    JACS - Journal of the American Chemical Society 2023. doi:10.1021/jacs.2c07674
  • Gomes, P. S. F. C., Gomes, D. E. B.,; Bernardi, R. C.
    Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy.
    Frontiers in Bioinformatics. 2022;(2). doi:10.3389/fbinf.2022.983306
  • Carvalho, Ruan M. ; Rosa, Iago G. L. ; Goliatt, Priscila V. Z. C. ; Gomes, Diego E. B. ; Goliatt, Leonardo.
    Prediction of Cyclodextrin Host-Guest Binding Through a Hybrid Support Vector Method.
    Advances in Intelligent Systems and Computing. 1ed.: Springer Singapore, (2021) v. , p. 309-317. doi: 10.1007/978-981-16-1543-6_30
  • Carvalho, RM. ; Rosa, IGL. ; Gomes, DEB. ; Goliatt, PVZC ; Goliatt, L.
    Gaussian processes regression for cyclodextrin host-guest binding prediction.
    Journal of Inclusion Phenomena and Macrocyclic Chemistry (2021), v. 101, p. 149-159. doi; 10.1007/s10847-021-01092-4
  • Montalvo-Acosta JJ, Pacak P. Gomes DEB, and Cecchini M.
    A Linear Interaction Energy Model for Cavitand Host–Guest Binding Affinities.
    The Journal of Physical Chemistry B, doi: (2018) doi:10.1021/acs.jpcb.8b03245.


  • Natividade, R.S.; Koehler M, Gomes P.S.F.C., Simpson J.D., Smith, S.C., Gomes D.E.B., de Lhoneux J., Yang J., Ray A, Dermody T.S., Bernardi R.C., Ogden, K. M., Alsteens D.
    Deciphering molecular mechanisms stabilizing the reovirus binding complex;
    PNAS - Proceedings of the National Academy of Sciences of the United States of America (2023). doi: 10.1073/pnas.2220741120
  • Gomes, Priscila S. F. C.; Forrester, Meredith; Pace, Margaret; Gomes, Diego E. B.; Bernardi, Rafael C.
    May the force be with you: The role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections.
    Frontiers in Chemistry (2023) doi: 10.3389/fchem.2023.1107427
  • Gomes, DEB; Melo, MCR; Gomes, PSFC; Bernardi, RC.
    Bridging the gap between in vitro and in silico single-molecule force spectroscopy.
    Bioarxv. doi: 10.1101/2022.07.14.500151


  • Gomes, D.E.B., Lins, R. D., Pascutti, P. G., Lei, C., Soares, T.A.;
    Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding.
    Journal of Physical Chemistry. B (2011). v.115, p.15389 - 15398.
  • Gomes, D.E.B., Lins, R. D., Pascutti, P. G., Lei, C., Soares, T. A.
    The Role of Nonbonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces.
    Journal of Physical Chemistry. B. (2010), v.114, p.531 - 540,
  • Gomes, D.E.B., R. D. Lins, Pascutti, P. G., Straatsma, T.P., Soares, T. A.
    Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase.
    Lecture Notes in Computer Science. (2008) v.5167, p.68 - 78, 2008.

Biomembranes and Local Anesthetics

  • Bernardi, R. C., Gomes, D.E.B., Gobato, R., Taft, C. A., Ota, A. T., Pascutti, P. G.
    Molecular dynamics study of biomembrane/local anesthetics interactions.
    Molecular Physics, v.107, p.1437 - 1443, 2009.
  • Bernardi, R. C., Gomes, D.E.B., Ito, A. S., Ota, A. T., Pascutti, P. G., Taft, C.
    Density functional and molecular dynamics simulations of local anesthetics in 0.9% NaCl solution.
    Molecular Simulation. (2007) v.33, p.1135 - 1141.
  • Bernardi, R. C., Gomes, D.E.B., Pascutti, P. G., Ito, A. S., Taft, C. A., Ota, A. T.
    Water solvent and local anesthetics: A computational study.
    International Journal of Quantum Chemistry.(2007) v.107, p.1642 - 1649.
  • Bernardi, R. C., Gomes, D.E.B., Pascutti, P. G., Ito, A. S., Ota, A. T.
    Theoretical studies on water-tetracaine interaction.
    International Journal of Quantum Chemistry. (2006) v.106, p.1277 - 1282.

Drug Discovery for Neglected Diseases

  • Hernández González, J. E., Salas-Sarduy, E., Hernández Alvarez, L., Gomes, D. E. B., Pascutti, P. G., Oostenbrink, C., & Leite, V. B. P.
    In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2.
    Journal of Computer-Aided Molecular Design (2021) ;35(10), 1067–1079. doi:10.1007/s10822-021-00420-7
  • Hernández L.A., Hernández J.E.G., Gomes, D.E.B., Pascutti PG.
    Dissecting a novel allosteric mechanism of cruzain: a computer-aided approach.
    PLOS One 14(1). (2019) doi:10.1371/journal.pone.0211227
  • Hernández L.A., Naranjo F.D., Hernández J.E.G., Soares R.O., Gomes, D.E.B., Pascutti PG.
    Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through in Silico Approaches.
    PLoS Neglected Tropical Diseases. (2015) v.9, p.e0003759.


  • Vieira, I. P. v., Cordeiro, G. T., Gomes, D. E. B., Melani, R. D., Vilela, L. F., Domont, G. B., Mesquita, R. D., Eleutherio, E. C. A., & Neves, B. C.
    Understanding xylose isomerase from Burkholderia cenocepacia: insights into structure and functionality for ethanol production.
    AMB Express (2019), 9(1), 73. doi:10.1186/s13568-019-0795-4