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Pedro Lopes

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentComputer Science
AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Veillette JP, Chao AF, Nith R, Lopes P, Nusbaum HC. Overlapping Cortical Substrate of Biomechanical Control and Subjective Agency. J Neurosci. 2025 Mar 24. PMID: 40127938; PMCID: PMC12044032.
      Citations:    Fields:    
    2. Veillette JP, Lopes P, Nusbaum HC. Temporal Dynamics of Brain Activity Predicting Sense of Agency over Muscle Movements. J Neurosci. 2023 11 15; 43(46):7842-7852. PMID: 37722848; PMCID: PMC10648515.
      Citations: 5     Fields:    Translation:Humans
    3. Su Q, Zou Q, Li Y, Chen Y, Teng SY, Kelleher JT, Nith R, Cheng P, Li N, Liu W, Dai S, Liu Y, Mazursky A, Xu J, Jin L, Lopes P, Wang S. A stretchable and strain-unperturbed pressure sensor for motion interference-free tactile monitoring on skins. Sci Adv. 2021 Nov 26; 7(48):eabi4563. PMID: 34818045; PMCID: PMC8612682.
      Citations: 46     Fields:    
    4. Lin FY, Lopes PEM, Harder E, MacKerell AD, Roux B. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J Chem Inf Model. 2018 05 29; 58(5):993-1004. PMID: 29624370; PMCID: PMC5975207.
      Citations: 24     Fields:    Translation:Cells
    5. Astudillo L, Da Silva TG, Wang Z, Han X, Jin K, VanWye J, Zhu X, Weaver K, Oashi T, Lopes PE, Orton D, Neitzel LR, Lee E, Landgraf R, Robbins DJ, MacKerell AD, Capobianco AJ. The Small Molecule IMR-1 Inhibits the Notch Transcriptional Activation Complex to Suppress Tumorigenesis. Cancer Res. 2016 06 15; 76(12):3593-603. PMID: 27197169; PMCID: PMC4911243.
      Citations: 47     Fields:    Translation:HumansAnimalsCells
    6. Lopes PE, Guvench O, MacKerell AD. Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2015; 1215:47-71. PMID: 25330958; PMCID: PMC4554537.
      Citations: 52     Fields:    Translation:Cells
    7. Huang J, Lopes PE, Roux B, MacKerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett. 2014 Sep 18; 5(18):3144-3150. PMID: 25247054; PMCID: PMC4167036.
      Citations: 59     Fields:    
    8. Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput. 2013 Dec 10; 9(12):5430-5449. PMID: 24459460; PMCID: PMC3896220.
      Citations: 141     Fields:    
    9. He X, Lopes PE, Mackerell AD. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers. 2013 Oct; 99(10):724-38. PMID: 23703219; PMCID: PMC3902549.
      Citations: 27     Fields:    Translation:Cells
    10. Lin B, Lopes PE, Roux B, MacKerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys. 2013 Aug 28; 139(8):084509. PMID: 24007020; PMCID: PMC3772949.
      Citations: 16     Fields:    Translation:Cells
    11. Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B. 2013 Aug 08; 117(31):9142-60. PMID: 23841725; PMCID: PMC3799809.
      Citations: 80     Fields:    Translation:Cells
    12. Hom K, Heinzl GA, Eakanunkul S, Lopes PE, Xue F, MacKerell AD, Wilks A. Small molecule antivirulents targeting the iron-regulated heme oxygenase (HemO) of P. aeruginosa. J Med Chem. 2013 Mar 14; 56(5):2097-109. PMID: 23379514; PMCID: PMC3643010.
      Citations: 17     Fields:    Translation:AnimalsCells
    13. Yu W, Lopes PE, Roux B, MacKerell AD. Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys. 2013 Jan 21; 138(3):034508. PMID: 23343286; PMCID: PMC3562330.
      Citations: 57     Fields:    Translation:Cells
    14. Zhu X, Lopes PE, Shim J, Mackerell AD. Correction to intrinsic energy landscapes of amino acid side-chains. J Chem Inf Model. 2012 Aug 27; 52(8):2317-8. PMID: 22809108; PMCID: PMC3428431.
      Citations: 1     Fields:    
    15. Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone f, ? and side-chain ?(1) and ?(2) dihedral angles. J Chem Theory Comput. 2012 Sep 11; 8(9):3257-3273. PMID: 23341755; PMCID: PMC3549273.
      Citations: 1837     Fields:    
    16. Zhu X, Lopes PE, Shim J, MacKerell AD. Intrinsic energy landscapes of amino acid side-chains. J Chem Inf Model. 2012 Jun 25; 52(6):1559-72. PMID: 22582825; PMCID: PMC3398815.
      Citations: 11     Fields:    Translation:Cells
    17. Zhu X, Lopes PE, Mackerell AD. Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci. 2012 Jan; 2(1):167-185. PMID: 23066428; PMCID: PMC3468154.
      Citations: 71     
    18. West AL, St John F, Lopes PE, MacKerell AD, Pozharski E, Michel SL. Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites. J Am Chem Soc. 2010 Oct 20; 132(41):14447-56. PMID: 20863122; PMCID: PMC2958704.
      Citations: 17     Fields:    Translation:Cells
    19. Baker CM, Lopes PE, Zhu X, Roux B, Mackerell AD. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput. 2010 Mar 01; 6(4):1181-1198. PMID: 20401166; PMCID: PMC2853947.
      Citations: 58     Fields:    
    20. Lopes PE, Lamoureux G, Mackerell AD. Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem. 2009 Sep; 30(12):1821-38. PMID: 19090564; PMCID: PMC2704921.
      Citations: 27     Fields:    
    21. Lopes PE, Roux B, Mackerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc. 2009 Sep; 124(1-2):11-28. PMID: 20577578; PMCID: PMC2888514.
      Citations: 78     
    22. Lopes PE, Lamoureux G, Roux B, Mackerell AD. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B. 2007 Mar 22; 111(11):2873-85. PMID: 17388420; PMCID: PMC2519011.
      Citations: 55     Fields:    
    23. Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. J Chem Theory Comput. 2006 Nov; 2(6):1587-97. PMID: 26627029.
      Citations: 48     Fields:    
    24. Lopes PE, Murashov V, Tazi M, Demchuk E, Mackerell AD. Development of an empirical force field for silica. Application to the quartz-water interface. J Phys Chem B. 2006 Feb 16; 110(6):2782-92. PMID: 16471886; PMCID: PMC2531191.
      Citations: 16     Fields:    
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