Publications

ResearcherID: C-5699-2008                                                     Research Scholar

1. I. Ivani, et. al. Parmbsc1: A refined force-field for DNA simulations. Nature Methods (2015). Just Accepted.
2. Perez, A., MacCallum, J.L., Brini, E., Simmerling, C. and Dill, K.A. A grid- based backbone correction to the ff12SB protein force field for implicit-solvent simulations” J Chem Theory Comput (2015). 10.1021/acs.jctc.5b00662
3. Perez, A.*, MacCallum, J. L.* and Dill, K. Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proc. Natl. Acad. Sci. U.S.A. (2015). doi:10.1073/pnas.1515561112
4. Toledo, A., Perez, A., Coleman, J. L. and Benach, J. L. The lipid raft proteome of Borrelia burgdorferi. Proteomics (2015). doi:10.1002/pmic.201500093
5. Nguyen, H., Perez, A., Bermeo, S. and Simmerling, C. Refinement of General- ized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. J Chem Theory Comput 11, 3714-3728 (2015).
6. J.L MacCallum*, A. Perez*, K.A. Dill, Determining protein structures by com- bining semireliable data with atomistic physical models by Bayesian inference (2015) Proc. Natl. Acad. Sci. U.S.A. 112, 6985-6990 (2015). * indicates equal contribution
7. Pasi, M. et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acid Research 42, 12272- 12283 (2014).
8. Perez, A. et al. Extracting representative structures from protein conforma- tional ensembles. Proteins: structure, function and bioinformatics 82, 2671- 2680 (2014).
9. Roy, A., Perez, A., Dill, K. A. and MacCallum, J. L. Computing the Rela- tive Stabilities and the Per Residue Components in Protein Conformational Changes. Structure 22, 168-175 (2013).
10. Candotti, M. et al. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS Comput. Biol. 9, e1003393 (2013).
11. Drsata, T. et al. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput 9, 707-721 (2013).
12. Dans, P. D., Perez, A., Faustino, I., Lavery, R. and Orozco, M. Exploring poly- morphisms in B-DNA helical conformations. Nucleic Acids Res. 40, 10668- 10678 (2012).
13. Perez, A. et al. Impact of methylation on the physical properties of DNA. Biophys. J. 102, 2140-2148 (2012).
14. Perez, A., Luque, F. J. and Orozco, M. Frontiers in molecular dynamics simu- lations of DNA. Acc. Chem. Res. 45, 196-205 (2012).
15. Perez, A., Yang, Z., Bahar, I. and Dill, K. A. FlexE: using elastic network models to compare models of protein structure. J Chem Theory Comput 8, 3985-3991 (2012).
16. Deniz, O. et al. Physical properties of naked DNA influence nucleosome po- sitioning and correlate with transcription start and termination sites in yeast. BMC Genomics 12, 489 (2011).
17. MacCallum, J. L. et al. Assessment of protein structure refinement in CASP9. Proteins 79 Suppl 10, 74-90 (2011).
18. Meyer, T. et al. MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure 18, 1399-1409 (2010).
19. Faustino, I., Perez, A. and Orozco, M. Toward a consensus view of duplex RNA flexibility. Biophys. J. 99, 1876-1885 (2010).
20. Perez, A. and Orozco, M. Real-time atomistic description of DNA unfolding. Angew. Chem. Int. Ed. Engl. 49, 4805-4808 (2010).
21. Lavery, R. et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B- DNA. Nucleic Acids Res. 38, 299-313 (2010).
22. Goni, J. R., Fenollosa, C., Perez, A., Torrents, D. and Orozco, M. DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinformatics 24, 1731-1732 (2008).
23. Svozil, D. et al. Geometrical and electronic structure variability of the sugar- phosphate backbone in nucleic acids. J Phys Chem B 112, 8188-8197 (2008).
24. Gros, J. et al. 8-Amino guanine accelerates tetramolecular G-quadruplex for- mation. Chem. Commun. (Camb.) 2926-2928 (2008). doi:10.1039/b801221k
25. Orozco, M., Noy, A. and Perez, A. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr. Opin. Struct. Biol. 18, 185-193 (2008).
26. Perez, A., Lankas, F., Luque, F. J. and Orozco, M. Towards a molecular dy- namics consensus view of B-DNA flexibility. Nucleic Acids Res. 36, 2379-2394 (2008).
27. Perez, A., Luque, F. J. and Orozco, M. Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc. 129, 14739-14745 (2007).
28. Perez, A. et al. Refinement of the AMBER force field for nucleic acids: im- proving the description of alpha/gamma conformers. Biophys. J. 92, 3817-3829 (2007).
29. Rueda, M. et al. A consensus view of protein dynamics. Proc. Natl. Acad. Sci. U.S.A. 104, 796-801 (2007).
30. Goi, J. R., Perez, A., Torrents, D. and Orozco, M. Determining promoter lo- cation based on DNA structure first-principles calculations. Genome Biol. 8, R263 (2007).
31. Noy, A., Perez, A., Laughton, C. A. and Orozco, M. Theoretical study of large conformational transitions in DNA: the BA conformational change in water and ethanol/water. Nucleic Acids Res. 35, 3330-3338 (2007).
32. Meyer, T. et al. Essential Dynamics: A Tool for Efficient Trajectory Compres- sion and Management. J Chem Theory Comput 2, 251-258 (2006).
33. Noy, A. et al. Data mining of molecular dynamics trajectories of nucleic acids. J. Biomol. Struct. Dyn. 23, 447-456 (2006).
34. Perez, A. et al. Exploring the Essential Dynamics of B-DNA. J Chem Theory Comput 1, 790-800 (2005).
35. Perez, A. et al. Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study. Chemistry 11, 5062-5066 (2005).
36. Noy, A., Perez, A., Mrquez, M., Luque, F. J. and Orozco, M. Structure, recog- nition properties, and flexibility of the DNA.RNA hybrid. J. Am. Chem. Soc. 127, 4910-4920 (2005).
37. Noy, A., Perez, A., Lankas, F., Javier Luque, F. and Orozco, M. Relative flex- ibility of DNA and RNA: a molecular dynamics study. J. Mol. Biol. 343, 627-638 (2004).
38. Perez, A., Noy, A., Lankas, F., Luque, F. J. and Orozco, M. The relative flex- ibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res. 32, 6144-6151 (2004).
39. Orozco, M., Perez, A., Noy, A. and Luque, F. J. Theoretical methods for the simulation of nucleic acids. Chem Soc Rev 32, 350 (2003).
 

Advertisements