Publications
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2015. The adaptive biasing force method: everything you always wanted to know but were afraid to ask.. J. Phys. Chem. B. 119:1129–51.
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1986. Active sites of the endo-beta-1,3-glucanases from Spisula sacchalinensis and Chlyamys albidys. Bioorg. Chem.. 12:1478–1483.
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1998. Accurate DNA dynamics without accurate long range electrostatics. J. Am. Chem. Soc.. 120:10928–10937.
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2006. Accounting for loop flexibility during protein-protein docking. Proteins. 62:956–969.
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2011. Accounting for large amplitude protein deformation during in silico macromolecular docking. Int. J. Mol. Sci.. 12:1316–33.
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2017. Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects. J Phys Chem B.
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2015. Ab initio RNA folding. Journal of Physics-condensed Matter. 27:233102.
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1999. Ab initio prediction of polypeptide structure from its sequence. Comput. Phys. Commun.. 122:139–140.
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2000. Ab initio polypeptide structure prediction. Theor. Chem. Acc.. 104:1–6.
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2006. Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. International Conference on Computational Science and its Applications (ICCSA 2006). 3984:222–231.
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2014. Wide Exploration of OPEP Protein Energy Landscapes using Advanced Monte Carlo Methods. Biophys. J.. 106:256A.
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2015. What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers. Biophys. J.. 108:204A-204A.
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2008. A VR Framework for Interacting with Molecular Simulations. Symposium on Virtual Reality Software and Technology (ACM-VRST 2008). :91–94.
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2015. Visualization of Biomolecular Structures: State of the Art. Eurographics Conference on Visualization (EuroVis) - STARs.
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2004. Visualization and Exploration of Factual and Textual Genomic Data. Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM 2004).
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2006. Visual Mining for Microarray Knowledge Discovery. International Conference on Information & Communication Technologies: from Theory to Applications (ICTTA 2006 - IEEE).
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2005. Visual data mining of genomic databases by immersive graph-based exploration. international Conference on Computer Graphics and interactive Techniques in Australasia and South East Asia (GRAPHITE 2005 - ACM-ACMSIGRAPH Sponsored). :143–146.
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2008. User Needs Analysis to Design a 3D Multimodal Protein-Docking Interface. Symposium on 3D User Interfaces 2008 (3DUI 2008 - IEEE). :125–132.
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2014. UnityMol: Interactive scientific visualization for integrative biology. Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on. :109–110.
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2015. UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :1–6.
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2016. Toward Microscopic Simulations of Proteins in Cell-Like Environments. Biophys. J.. 110:386A.
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2002. Spatial order in liquid crystals: Computer simulations of systems of ellipsoids. MORPHOLOGY OF CONDENSED MATTER: PHYSICS AND GEOMETRY OF SPATIALLY COMPLEX SYSTEMS. 600:172–186.
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2008. Simulating the early steps of amyloid fibril formation and disassembly. Publication Series of the John von Neumann Institute for Computing NIC Series. 40:7–12.
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2000. Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores. Proceedings of the Euradwaste 1999 conference. :390–393.