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Overview on Agent-Based Social Modelling and the use of formal languages. Formal Languages for Computer Simulation: Transdisciplinary Models and Applications 333-377 (2013).doi:10.4018/978-1-4666-4369-7.ch011
Toward an atomistic description of the urea-denatured state of proteins. Proceedings of the National Academy of Sciences of the United States of America 110, 5933-8 (2013).
Established and emerging trends in computational drug discovery in the structural genomics era. Chemistry & biology 19, 29-41 (2012).
H-bond network optimization in protein-protein complexes: are all-atom force field scores enough?. Proteins 80, 818-24 (2012).
Theory and simulation: complexity and emergence. Current opinion in structural biology 22, 127-9 (2012).
pyDockCG: new coarse-grained potential for protein-protein docking. The journal of physical chemistry. B 115, 6032-9 (2011).
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. Journal of computational chemistry 31, 1224-35 (2010).
Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan. The Journal of biological chemistry 284, 3106-16 (2009).
Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis. The Journal of biological chemistry 284, 14457-68 (2009).
Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N. Journal of the American Chemical Society 130, 1688-93 (2008).
Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases. Proceedings of the National Academy of Sciences of the United States of America 105, 16918-23 (2008).
Nitric oxide reactivity with globins as investigated through computer simulation. Methods in enzymology 437, 477-98 (2008).
Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of molecular biology 337, 227-39 (2004).
Proton-transfer dynamics in the activation of cytochrome P450eryF. Journal of the American Chemical Society 124, 1430-7 (2002).