Lalith Perera, Ph.D. - Publications

Affiliations: 
GISBL NIEHS/NIH, Durham, NC, United States 
Area:
Computational Chemistry
Website:
https://www.niehs.nih.gov/research/atniehs/facilities/compmole/index.cfm

151 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. Author Correction: Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nature Structural & Molecular Biology. PMID 38196035 DOI: 10.1038/s41594-024-01213-w  0.588
2024 Min J, Keswani T, LaHood NA, Lytle IR, Marini-Rapoport O, Andrieux L, Sneed SL, Edwards LL, Petrovich RM, Perera L, Pomés A, Pedersen LC, Patil SU, Mueller GA. Design of an Ara h 2 hypoallergen from conformational epitopes. Clinical and Experimental Allergy : Journal of the British Society For Allergy and Clinical Immunology. PMID 38168500 DOI: 10.1111/cea.14433  0.392
2023 Kirby TW, Gabel SA, DeRose EF, Perera L, Krahn JM, Pedersen LC, London RE. Targeting the Structural Maturation Pathway of HIV-1 Reverse Transcriptase. Biomolecules. 13. PMID 38002285 DOI: 10.3390/biom13111603  0.585
2023 Li L, Perera L, Varghese SA, Shiloh-Malawsky Y, Hunter SE, Sneddon TP, Powell CM, Matera AG, Fan Z. A homozygous missense variant in the YG box domain in an individual with severe spinal muscular atrophy: a case report and variant characterization. Frontiers in Cellular Neuroscience. 17: 1259380. PMID 37841286 DOI: 10.3389/fncel.2023.1259380  0.414
2023 Lee EY, Choi W, Burkholder AB, Perera L, Mack JA, Miller FW, Fessler MB, Cook DN, Karmaus PWF, Nakano H, Garantziotis S, Madenspacher JH, House JS, Akhtari FS, Schmitt CS, et al. Race/ethnicity-stratified fine-mapping of the MHC locus reveals genetic variants associated with late-onset asthma Frontier Genetics. 14: 1173676. PMID 37415598 DOI: 10.3389/fgene.2023.1173676.  0.206
2023 Hayne CK, Butay KJU, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nature Structural & Molecular Biology. PMID 37231153 DOI: 10.1038/s41594-023-00991-z  0.641
2023 Min J, Foo ACY, Gabel SA, Perera L, DeRose EF, Pomés A, Pedersen LC, Mueller GA. Structural and ligand binding analysis of the pet allergens Can f 1 and Fel d 7. Frontiers in Allergy. 4: 1133412. PMID 36960093 DOI: 10.3389/falgy.2023.1133412  0.461
2022 Karaj E, Sindi SH, Kuganesan N, Perera L, Taylor W, Tillekeratne LMV. Tunable Cysteine-Targeting Electrophilic Heteroaromatic Warheads Induce Ferroptosis. Journal of Medicinal Chemistry. PMID 35984756 DOI: 10.1021/acs.jmedchem.2c00909  0.271
2022 Fu Y, da Fonseca Rezende E Mello J, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, et al. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. Plos One. 17: e0272364. PMID 35947606 DOI: 10.1371/journal.pone.0272364  0.309
2022 Riccio AA, Bouvette J, Perera L, Longley MJ, Krahn JM, Williams JG, Dutcher R, Borgnia MJ, Copeland WC. Structural insight and characterization of human Twinkle helicase in mitochondrial disease. Proceedings of the National Academy of Sciences of the United States of America. 119: e2207459119. PMID 35914129 DOI: 10.1073/pnas.2207459119  0.282
2022 Bienstock RJ, Perera L, Pasquinelli MA. Molecular Modeling Study of the Genotoxicity of the Sudan I and Sudan II Azo Dyes and Their Metabolites. Frontiers in Chemistry. 10: 880782. PMID 35815205 DOI: 10.3389/fchem.2022.880782  0.298
2022 Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB. A structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Nature Communications. 13: 2231. PMID 35468885 DOI: 10.1038/s41467-022-29673-y  0.36
2022 Karaj E, Dlamini S, Koranne R, Sindi SH, Perera L, Taylor WR, Viranga Tillekeratne LM. Pharmacophore optimization of imidazole chalcones to modulate microtubule dynamics. Bioorganic Chemistry. 122: 105700. PMID 35313238 DOI: 10.1016/j.bioorg.2022.105700  0.314
2022 Dahl JM, Thomas N, Tracy MA, Hearn BL, Perera L, Kennedy SR, Herr AJ, Kunkel TA. Probing the mechanisms of two exonuclease domain mutators of DNA polymerase ϵ. Nucleic Acids Research. PMID 35037018 DOI: 10.1093/nar/gkab1255  0.274
2021 Fu Y, Mello JDFRE, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, et al. The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 34729560 DOI: 10.1101/2021.10.22.465476  0.302
2021 Bai W, Wells ML, Lai WS, Hicks SN, Burkholder AB, Perera L, Kimmel AR, Blackshear PJ. A post-transcriptional regulon controlled by TtpA, the single tristetraprolin family member expressed in Dictyostelium discoideum. Nucleic Acids Research. PMID 34718768 DOI: 10.1093/nar/gkab983  0.518
2021 Al-Hamashi AA, Koranne R, Dlamini S, Alqahtani A, Karaj E, Rashid MS, Knoff JR, Dunworth M, Pflum MKH, Casero RA, Perera L, Taylor WR, Tillekeratne LMV. A new class of cytotoxic agents targets tubulin and disrupts microtubule dynamics. Bioorganic Chemistry. 116: 105297. PMID 34509798 DOI: 10.1016/j.bioorg.2021.105297  0.263
2021 Gustafson MA, Perera L, Shi M, Copeland WC. Mechanisms of SSBP1 variants in mitochondrial disease: Molecular dynamics simulations reveal stable tetramers with altered DNA binding surfaces. Dna Repair. 107: 103212. PMID 34464898 DOI: 10.1016/j.dnarep.2021.103212  0.339
2021 Jamsen JA, Sassa A, Perera L, Shock DD, Beard WA, Wilson SH. Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair. Nature Communications. 12: 5055. PMID 34417448 DOI: 10.1038/s41467-021-24486-x  0.475
2021 Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE. Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U. Nucleic Acids Research. PMID 34403466 DOI: 10.1093/nar/gkab719  0.625
2021 Sinha BK, Perera L, Cannon RE. NCX-4040, a Unique Nitric Oxide Donor, Induces Reversal of Drug-Resistance in Both ABCB1- and ABCG2-Expressing Multidrug Human Cancer Cells. Cancers. 13. PMID 33918289 DOI: 10.3390/cancers13071680  0.23
2021 Kim K, Kirby TW, Perera L, London RE. Phosphopeptide interactions of the Nbs1 N-terminal FHA-BRCT1/2 domains. Scientific Reports. 11: 9046. PMID 33907233 DOI: 10.1038/s41598-021-88400-7  0.56
2021 Foo ACY, Thompson PM, Chen SH, Jadi R, Lupo B, DeRose EF, Arora S, Placentra VC, Premkumar L, Perera L, Pedersen LC, Martin N, Mueller GA. The mosquito protein AEG12 displays both cytolytic and antiviral properties via a common lipid transfer mechanism. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33688047 DOI: 10.1073/pnas.2019251118  0.466
2021 Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, et al. Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nature Communications. 12: 636. PMID 33504779 DOI: 10.1038/s41467-020-20608-z  0.651
2020 Banerjee R, Perera L, Tillekeratne LMV. Potential SARS-CoV-2 main protease inhibitors. Drug Discovery Today. PMID 33309533 DOI: 10.1016/j.drudis.2020.12.005  0.254
2020 Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, et al. Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15. Biorxiv : the Preprint Server For Biology. PMID 32803198 DOI: 10.1101/2020.08.11.244863  0.622
2020 Perera L, Beard WA, Pedersen LG, Shock DD, Wilson SH. Preferential DNA Polymerase β Reverse Reaction with Imidodiphosphate. Acs Omega. 5: 15317-15324. PMID 32637805 DOI: 10.1021/acsomega.0c01345  0.6
2020 Li Y, Hamilton KJ, Perera L, Wang T, Gruzdev A, Jefferson TB, Zhang AX, Mathura E, Gerrish KE, Wharey L, Martin NP, Li JL, Korach KS. ESR1 mutations associated with EIS change conformation of ligand receptor complex and alter transcriptome profile. Endocrinology. PMID 32242619 DOI: 10.1210/Endocr/Bqaa050  0.572
2019 Pedersen LC, Inoue K, Kim S, Perera L, Shaw ND. A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1. Communications Biology. 2: 255. PMID 31925095 DOI: 10.1038/s42003-019-0499-y  0.502
2019 Foo ACY, Thompson PM, Perera L, Arora S, DeRose EF, Williams J, Mueller GA. Hydrophobic ligands influence the structure, stability, and processing of the major cockroach allergen Bla g 1. Scientific Reports. 9: 18294. PMID 31797892 DOI: 10.1038/S41598-019-54689-8  0.425
2019 Shizu R, Yokobori K, Perera L, Pedersen L, Negishi M. Ligand induced dissociation of the AR homodimer precedes AR monomer translocation to the nucleus. Scientific Reports. 9: 16734. PMID 31723170 DOI: 10.1038/S41598-019-53139-9  0.659
2019 Sinha BK, Perera L, Cannon RE. Reversal of drug resistance by JS-K and nitric oxide in ABCB1- and ABCG2-expressing multi-drug resistant human tumor cells. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie. 120: 109468. PMID 31605952 DOI: 10.1016/J.Biopha.2019.109468  0.342
2019 Gustafson MA, McCormick EM, Perera L, Longley MJ, Bai R, Kong J, Dulik M, Shen L, Goldstein AC, McCormack SE, Laskin BL, Leroy BP, Ortiz-Gonzalez XR, Ellington MG, Copeland WC, et al. Mitochondrial single-stranded DNA binding protein novel de novo SSBP1 mutation in a child with single large-scale mtDNA deletion (SLSMD) clinically manifesting as Pearson, Kearns-Sayre, and Leigh syndromes. Plos One. 14: e0221829. PMID 31479473 DOI: 10.1371/Journal.Pone.0221829  0.393
2019 Pelch KE, Li Y, Perera L, Thayer KA, Korach KS. Characterization of Estrogenic and Androgenic Activities for Bisphenol A-like Chemicals (BPs): In Vitro Estrogen and Androgen Receptors Transcriptional Activation, Gene Regulation, and Binding Profiles. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 31388671 DOI: 10.1093/Toxsci/Kfz173  0.575
2019 Pedersen LC, Inoue K, Kim S, Perera L, Shaw ND. A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1. Communications Biology. 2: 255. PMID 31312724 DOI: 10.1038/s42003-019-0499-y  0.502
2019 Alofe O, Kisanga E, Inayat-Hussain SH, Fukumura M, Garcia-Milian R, Perera L, Vasiliou V, Whirledge S. Determining the endocrine disruption potential of industrial chemicals using an integrative approach: Public databases, in vitro exposure, and modeling receptor interactions. Environment International. 131: 104969. PMID 31310931 DOI: 10.1016/J.Envint.2019.104969  0.373
2019 Lai WS, Wells ML, Perera L, Blackshear PJ. The tandem zinc finger RNA binding domain of members of the tristetraprolin protein family. Wiley Interdisciplinary Reviews. Rna. e1531. PMID 30864256 DOI: 10.1002/Wrna.1531  0.577
2019 Li Y, Hamilton K, Wang T, Perera L, Zhang A, Jefferson T, Mathura E, Gerrish K, Wharey L, Gruzdev A, Martin N, Li J, Korach K. SAT-205 ESR1 Q375H and R394H Mutants Associated with Estrogen Insensitivity Syndrome Mediate Genome-Wide Genetic and Epigenetic Aberrances Journal of the Endocrine Society. 3. DOI: 10.1210/Js.2019-Sat-205  0.311
2019 Foo AC, Thompson PM, Arora S, DeRose EF, Perera L, Mueller GA. Influence of Hydrophobic Cargo Binding on the Structure, Stability, and Allergenicity of the Cockroach Allergen Bla g 1 Journal of Allergy and Clinical Immunology. 143: AB213. DOI: 10.1016/J.Jaci.2018.12.649  0.398
2018 Samaradivakara SP, Samarasekera R, Handunnetti SM, Weerasena OVDSJ, Al-Hamashi AA, Slama JT, Taylor WR, Alhadidi Q, Shah ZA, Perera L, Tillekeratne LMV. A Bioactive Resveratrol Trimer from the Stem Bark of the Sri Lankan Endemic Plant Vateria copallifera. Journal of Natural Products. PMID 30040425 DOI: 10.1021/Acs.Jnatprod.7B00892  0.353
2018 Jongwattanapisan P, Terajima M, Miguez PA, Querido W, Nagaoka H, Sumida N, Gurysh EG, Ainslie KM, Pleshko N, Perera L, Yamauchi M. Identification of the effector domain of biglycan that facilitates BMP-2 osteogenic function. Scientific Reports. 8: 7022. PMID 29728612 DOI: 10.1038/S41598-018-25279-X  0.372
2018 Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, Myers P, Perera L, Tucker CJ, Perou CM, Wade PA. GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nature Communications. 9: 1059. PMID 29535312 DOI: 10.1038/S41467-018-03478-4  0.457
2018 Min J, Perera L, Krahn JM, Jewell CM, Moon AF, Cidlowski JA, Pedersen LC. Probing Dominant Negative Behavior of Glucocorticoid Receptor β through a Hybrid Structural and Biochemical Approach. Molecular and Cellular Biology. PMID 29437838 DOI: 10.1128/Mcb.00453-17  0.567
2018 Li Y, Perera L, Coons LA, Burns KA, Tyler Ramsey J, Pelch KE, Houtman R, van Beuningen R, Teng CT, Korach KS. Differential in Vitro Biological Action, Coregulator Interactions, and Molecular Dynamic Analysis of Bisphenol A (BPA), BPAF, and BPS Ligand-ERα Complexes. Environmental Health Perspectives. 126: 017012. PMID 29389661 DOI: 10.1289/Ehp2505  0.578
2017 Zheng X, Mueller GA, Kiim K, Perera L, DeRose EF, London RE. Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase. The Biochemical Journal. PMID 28811321 DOI: 10.1042/Bcj20170480  0.594
2017 Perera L, Li Y, Coons LA, Houtman R, van Beuningen R, Goodwin B, Auerbach SS, Teng CT. Binding of bisphenol A, bisphenol AF, and bisphenol S on the androgen receptor: Coregulator recruitment and stimulation of potential interaction sites. Toxicology in Vitro : An International Journal Published in Association With Bibra. PMID 28751236 DOI: 10.1016/J.Tiv.2017.07.020  0.387
2017 Shizu R, Osabe M, Perera L, Moore R, Sueyoshi T, Negishi M. Phosphorylated nuclear receptor CAR forms a homodimer to repress its constitutive activity for ligand activation. Molecular and Cellular Biology. PMID 28265001 DOI: 10.1128/Mcb.00649-16  0.578
2017 Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH. Revealing the role of the product metal in DNA polymerase β catalysis. Nucleic Acids Research. PMID 28108654 DOI: 10.1093/Nar/Gkw1363  0.645
2017 Wells ML, Perera L, Blackshear PJ. An Ancient Family of RNA-Binding Proteins: Still Important! Trends in Biochemical Sciences. PMID 28096055 DOI: 10.1016/J.Tibs.2016.12.003  0.558
2016 Perera L, Beard WA, Pedersen LG, Wilson SH. Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites. Inorganic Chemistry. PMID 27976880 DOI: 10.1021/Acs.Inorgchem.6B02189  0.648
2016 Almaliti J, Al-Hamashi AA, Negmeldin AT, Hanigan CL, Perera L, Pflum MK, Casero RA, Tillekeratne LM. Largazole Analogues Embodying Radical Changes in the Depsipeptide Ring: Development of a More Selective and Highly Potent Analogue. Journal of Medicinal Chemistry. PMID 27809521 DOI: 10.1021/Acs.Jmedchem.6B01271  0.724
2016 Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS. Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Nucleic Acids Research. PMID 27060144 DOI: 10.1093/Nar/Gkw228  0.411
2016 Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biology. 17: 36. PMID 26922637 DOI: 10.1186/S13059-016-0897-0  0.374
2016 Mueller G, Randall TA, Glesner J, Pedersen L, Perera L, Edwards LL, DeRose E, Chapman MD, London R, Pomés A. Structural, Serological, and Genomic Analyses of the Major Mite Allergen Der p 23 The Journal of Allergy and Clinical Immunology. 137. DOI: 10.1016/J.Jaci.2015.12.1014  0.616
2015 Mueller GA, Randall TA, Glesner J, Pedersen LC, Perera L, Edwards LL, DeRose EF, Chapman MD, London RE, Pomés A. Serological, genomic, and structural analyses of the major mite allergen Der p 23. Clinical and Experimental Allergy : Journal of the British Society For Allergy and Clinical Immunology. PMID 26602749 DOI: 10.1111/Cea.12680  0.632
2015 Perera L, Freudenthal BD, Beard WA, Shock DD, Pedersen LG, Wilson SH. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proceedings of the National Academy of Sciences of the United States of America. 112: E5228-36. PMID 26351676 DOI: 10.1073/Pnas.1511207112  0.646
2015 Wells ML, Hicks SN, Perera L, Blackshear PJ. Functional equivalence of an evolutionarily conserved RNA binding module. The Journal of Biological Chemistry. PMID 26292216 DOI: 10.1074/Jbc.M115.673012  0.567
2015 Zheng X, Perera L, Mueller GA, DeRose EF, London RE. Asymmetric conformational maturation of HIV-1 reverse transcriptase. Elife. 4. PMID 26037594 DOI: 10.7554/Elife.06359  0.519
2015 Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 517: 635-9. PMID 25409153 DOI: 10.1038/Nature13886  0.473
2015 Zheng X, Perera L, Mueller GA, DeRose EF, London RE. Author response: Asymmetric conformational maturation of HIV-1 reverse transcriptase Elife. DOI: 10.7554/Elife.06359.039  0.516
2015 Zheng X, Perera L, Mueller GA, DeRose EF, London RE. Asymmetric conformational maturation of HIV-1 reverse transcriptase Elife. 4: 1-24. DOI: 10.7554/eLife.06359  0.464
2015 Takaku M, Grimm SA, Shimbo T, Perera L, Machida S, Kurumizaka H, Wade PA. Abstract 964: GATA3 modulates chromatin structure to establish active enhancers in breast cancer cells Cancer Research. 75: 964-964. DOI: 10.1158/1538-7445.Am2015-964  0.379
2014 Perera L, Beard WA, Pedersen LG, Wilson SH. Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. Advances in Protein Chemistry and Structural Biology. 97: 83-113. PMID 25458356 DOI: 10.1016/Bs.Apcsb.2014.10.001  0.648
2014 Choi YJ, Lai WS, Fedic R, Stumpo DJ, Huang W, Li L, Perera L, Brewer BY, Wilson GM, Mason JM, Blackshear PJ. The Drosophila Tis11 protein and its effects on mRNA expression in flies. The Journal of Biological Chemistry. 289: 35042-60. PMID 25342740 DOI: 10.1074/Jbc.M114.593491  0.652
2014 Bhansali P, Hanigan CL, Perera L, Casero RA, Tillekeratne LM. Synthesis and biological evaluation of largazole analogues with modified surface recognition cap groups. European Journal of Medicinal Chemistry. 86: 528-41. PMID 25203782 DOI: 10.1016/J.Ejmech.2014.09.009  0.724
2014 Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 111: E2937-46. PMID 25002523 DOI: 10.1073/Pnas.1406381111  0.416
2014 Blackshear PJ, Perera L. Phylogenetic distribution and evolution of the linked RNA-binding and NOT1-binding domains in the tristetraprolin family of tandem CCCH zinc finger proteins. Journal of Interferon & Cytokine Research : the Official Journal of the International Society For Interferon and Cytokine Research. 34: 297-306. PMID 24697206 DOI: 10.1089/Jir.2013.0150  0.576
2014 Mueller GA, Ankney JA, Glesner J, Khurana T, Edwards LL, Pedersen LC, Perera L, Slater JE, Pomés A, London RE. Characterization of an anti-Bla g 1 scFv: epitope mapping and cross-reactivity. Molecular Immunology. 59: 200-7. PMID 24667070 DOI: 10.1016/J.Molimm.2014.02.003  0.628
2014 Liu C, Sheng J, Krahn JM, Perera L, Xu Y, Hsieh PH, Dou W, Liu J, Pedersen LC. Molecular mechanism of substrate specificity for heparan sulfate 2-O-sulfotransferase. The Journal of Biological Chemistry. 289: 13407-18. PMID 24652287 DOI: 10.1074/Jbc.M113.530535  0.537
2014 Lai WS, Perera L, Hicks SN, Blackshear PJ. Mutational and structural analysis of the tandem zinc finger domain of tristetraprolin. The Journal of Biological Chemistry. 289: 565-80. PMID 24253039 DOI: 10.1074/Jbc.M113.466326  0.596
2014 Blackshear PJ, Perera L. Phylogenetic distribution and evolution of the linked RNA-binding and NOT1-binding domains in the tristetraprolin family of tandem CCCH zinc finger proteins Journal of Interferon and Cytokine Research. 34: 297-306. DOI: 10.1089/jir.2013.0150  0.509
2013 Randall TA, Perera L, London RE, Mueller GA. Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin. Genome Biology and Evolution. 5: 2344-58. PMID 24253356 DOI: 10.1093/Gbe/Evt182  0.588
2013 Mutoh S, Sobhany M, Moore R, Perera L, Pedersen L, Sueyoshi T, Negishi M. Phenobarbital indirectly activates the constitutive active androstane receptor (CAR) by inhibition of epidermal growth factor receptor signaling. Science Signaling. 6: ra31. PMID 23652203 DOI: 10.1126/Scisignal.2003705  0.642
2013 Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH. Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. Journal of the American Chemical Society. 135: 8078-88. PMID 23647366 DOI: 10.1021/Ja403842J  0.737
2013 Perdivara I, Perera L, Sricholpech M, Terajima M, Pleshko N, Yamauchi M, Tomer KB. Unusual fragmentation pathways in collagen glycopeptides. Journal of the American Society For Mass Spectrometry. 24: 1072-81. PMID 23633013 DOI: 10.1007/S13361-013-0624-Y  0.399
2012 DeRose EF, Perera L, Murray MS, Kunkel TA, London RE. Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide. Biochemistry. 51: 2407-16. PMID 22390730 DOI: 10.1021/Bi201710Q  0.581
2012 Elking DM, Perera L, Pedersen LG. HPAM: Hirshfeld Partitioned Atomic Multipoles. Computer Physics Communications. 183: 390-397. PMID 22140274 DOI: 10.1016/J.Cpc.2011.10.003  0.491
2011 Elking DM, Perera L, Duke R, Darden T, Pedersen LG. A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank. Journal of Computational Chemistry. 32: 3283-95. PMID 21915883 DOI: 10.1002/Jcc.21914  0.66
2011 Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH. Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. The Journal of Biological Chemistry. 286: 31650-60. PMID 21733843 DOI: 10.1074/Jbc.M111.253401  0.657
2011 Schorzman AN, Perera L, Cutalo-Patterson JM, Pedersen LC, Pedersen LG, Kunkel TA, Tomer KB. Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry. Dna Repair. 10: 454-65. PMID 21354867 DOI: 10.1016/J.Dnarep.2011.01.010  0.668
2010 Elking DM, Perera L, Duke R, Darden T, Pedersen LG. Atomic forces for geometry-dependent point multipole and gaussian multipole models. Journal of Computational Chemistry. 31: 2702-13. PMID 20839297 DOI: 10.1002/Jcc.21563  0.666
2010 Butterfoss GL, DeRose EF, Gabel SA, Perera L, Krahn JM, Mueller GA, Zheng X, London RE. Conformational dependence of 13C shielding and coupling constants for methionine methyl groups. Journal of Biomolecular Nmr. 48: 31-47. PMID 20734113 DOI: 10.1007/S10858-010-9436-6  0.579
2009 Mutoh S, Osabe M, Inoue K, Moore R, Pedersen L, Perera L, Rebolloso Y, Sueyoshi T, Negishi M. Dephosphorylation of threonine 38 is required for nuclear translocation and activation of human xenobiotic receptor CAR (NR1I3). The Journal of Biological Chemistry. 284: 34785-92. PMID 19858220 DOI: 10.1074/Jbc.M109.048108  0.663
2009 Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA. Template strand scrunching during DNA gap repair synthesis by human polymerase lambda. Nature Structural & Molecular Biology. 16: 967-72. PMID 19701199 DOI: 10.1038/Nsmb.1654  0.524
2009 Hobbs CA, Deterding LJ, Perera L, Bobay BG, Thompson RJ, Darden TA, Cavanagh J, Tomer KB. Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Biochemistry. 48: 8603-14. PMID 19658395 DOI: 10.1021/Bi900350Q  0.632
2009 Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. Journal of the American Chemical Society. 131: 1550-6. PMID 19119875 DOI: 10.1021/Ja8082818  0.788
2008 Cisneros GA, Tholander SN, Parisel O, Darden TA, Elking D, Perera L, Piquemal JP. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. International Journal of Quantum Chemistry. 108: 1905-1912. PMID 19606279 DOI: 10.1002/Qua.21675  0.756
2008 Cisneros GA, Perera L, García-Díaz M, Bebenek K, Kunkel TA, Pedersen LG. Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies. Dna Repair. 7: 1824-34. PMID 18692600 DOI: 10.1016/J.Dnarep.2008.07.007  0.715
2008 Zaas AK, Liao G, Chien JW, Weinberg C, Shore D, Giles SS, Marr KA, Usuka J, Burch LH, Perera L, Perfect JR, Peltz G, Schwartz DA. Plasminogen alleles influence susceptibility to invasive aspergillosis. Plos Genetics. 4: e1000101. PMID 18566672 DOI: 10.1371/Journal.Pgen.1000101  0.332
2008 Tie JK, Zheng MY, Hsiao KL, Perera L, Stafford DW, Straight DL. Transmembrane domain interactions and residue proline 378 are essential for proper structure, especially disulfide bond formation, in the human vitamin K-dependent gamma-glutamyl carboxylase. Biochemistry. 47: 6301-10. PMID 18498174 DOI: 10.1021/Bi800235R  0.418
2008 Chandrasekaran V, Lee CJ, Duke RE, Perera L, Pedersen LG. Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling. Protein Science : a Publication of the Protein Society. 17: 1354-61. PMID 18493021 DOI: 10.1110/Ps.034801.108  0.794
2008 Croteau DL, DellaVecchia MJ, Perera L, Van Houten B. Cooperative damage recognition by UvrA and UvrB: identification of UvrA residues that mediate DNA binding. Dna Repair. 7: 392-404. PMID 18248777 DOI: 10.1016/J.Dnarep.2007.11.013  0.412
2008 Lee CJ, Lin P, Chandrasekaran V, Duke RE, Everse SJ, Perera L, Pedersen LG. Proposed structural models of human factor Va and prothrombinase. Journal of Thrombosis and Haemostasis : Jth. 6: 83-9. PMID 17973648 DOI: 10.1111/J.1538-7836.2007.02821.X  0.794
2008 Alhamadsheh MM, Gupta S, Hudson RA, Perera L, Tillekeratne LM. Total synthesis and selective activity of a new class of conformationally restrained epothilones. Chemistry (Weinheim An Der Bergstrasse, Germany). 14: 570-81. PMID 17955508 DOI: 10.1002/Chem.200701143  0.722
2008 Patterson K, Colina CM, Perera L, Pedersen LG. Human tissue factor: A molecular dynamics study Aiche Annual Meeting, Conference Proceedings 0.676
2007 Lee SJ, Perera L, Coulter SJ, Mohrenweiser HW, Jetten A, Goldstein JA. The discovery of new coding alleles of human CYP26A1 that are potentially defective in the metabolism of all-trans retinoic acid and their assessment in a recombinant cDNA expression system. Pharmacogenetics and Genomics. 17: 169-80. PMID 17460545 DOI: 10.1097/Fpc.0B013E32801152D6  0.339
2007 Lee CJ, Chandrasekaran V, Duke RE, Perera L, Pedersen LG. A proposed structural model of human protein Z. Journal of Thrombosis and Haemostasis : Jth. 5: 1558-61. PMID 17456189 DOI: 10.1111/J.1538-7836.2007.02597.X  0.774
2007 Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. Journal of Computational Chemistry. 28: 938-57. PMID 17253648 DOI: 10.1002/Jcc.20586  0.558
2007 Liu SB, Perera L, Pedersen LG. Binuclear manganese(II) complexes in biological systems Molecular Physics. 105: 2893-2898. DOI: 10.1080/00268970701747199  0.561
2006 Colina CM, Venkateswarlu D, Duke R, Perera L, Pedersen LG. What causes the enhancement of activity of factor VIIa by tissue factor? Journal of Thrombosis and Haemostasis : Jth. 4: 2726-9. PMID 17002651 DOI: 10.1111/J.1538-7836.2006.02222.X  0.753
2006 Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. The Journal of Chemical Physics. 125: 054511. PMID 16942230 DOI: 10.1063/1.2234774  0.783
2005 Perera L, Pedersen LG. A reconsideration of the evidence for structural reorganization in FVII zymogen. Journal of Thrombosis and Haemostasis : Jth. 3: 1543-5. PMID 15978118 DOI: 10.1111/J.1538-7836.2005.01433.X  0.565
2005 Herce DH, Perera L, Darden TA, Sagui C. Surface solvation for an ion in a water cluster. The Journal of Chemical Physics. 122: 024513. PMID 15638604 DOI: 10.1063/1.1829635  0.731
2005 Colina CM, Duke RE, Venkateswarlu D, Perera L, Darden T, Pedersen LG. Atomic molecular dynamical modeling of a large protein complex: Stf-fviia Aiche Annual Meeting, Conference Proceedings. 10513.  0.756
2004 Perera L, Darden TA, Duke RE, Venkateswarlu D, Pedersen LG. Early unfolding response of a stable protein domain to environmental changes Journal of Physical Chemistry A. 108: 9834-9840. DOI: 10.1021/Jp048385L  0.791
2003 Venkateswarlu D, Duke RE, Perera L, Darden TA, Pedersen LG. An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF-VIIa-Xa): a protein-protein docking and molecular dynamics refinement study. Journal of Thrombosis and Haemostasis : Jth. 1: 2577-88. PMID 14750502 DOI: 10.1111/J.1538-7836.2003.00421.X  0.812
2003 Gorokhov A, Negishi M, Johnson EF, Pedersen LC, Perera L, Darden TA, Pedersen LG. Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4. Biophysical Journal. 84: 57-68. PMID 12524265 DOI: 10.1016/S0006-3495(03)74832-2  0.792
2002 Perera L, Darden TA, Pedersen LG. Predicted solution structure of zymogen human coagulation FVII. Journal of Computational Chemistry. 23: 35-47. PMID 11913388 DOI: 10.1002/Jcc.1155  0.72
2002 Venkateswarlu D, Perera L, Darden T, Pedersen LG. Structure and dynamics of zymogen human blood coagulation factor X. Biophysical Journal. 82: 1190-206. PMID 11867437 DOI: 10.1016/S0006-3495(02)75476-3  0.805
2002 Bruce CD, Senapati S, Berkowitz ML, Perera L, Forbes MDE. Molecular dynamics simulations of sodium dodecyl sulfate micelle in water: The behavior of water Journal of Physical Chemistry B. 106: 10902-10907. DOI: 10.1021/Jp025872X  0.598
2002 Bruce CD, Berkowitz ML, Perera L, Forbes MDE. Molecular dynamics simulation of sodium dodecyl sulfate micelle in water: Micellar structural characteristics and counterion distribution Journal of Physical Chemistry B. 106: 3788-3793. DOI: 10.1021/Jp013616Z  0.62
2001 Perera L, Darden TA, Pedersen LG. Modeling human zymogen factor IX. Thrombosis and Haemostasis. 85: 596-603. PMID 11341491 DOI: 10.1055/S-0037-1615639  0.727
2001 Jin J, Perera L, Stafford D, Pedersen L. Four loops of the catalytic domain of factor VIIa mediate the effect of the first EGF-like domain substitution on factor VIIa catalytic activity Journal of Molecular Biology. 307: 1503-1517. PMID 11292356 DOI: 10.1006/Jmbi.2001.4556  0.603
2000 Perera L, Foley C, Darden TA, Stafford D, Mather T, Esmon CT, Pedersen LG. Modeling zymogen protein C. Biophysical Journal. 79: 2925-43. PMID 11106601 DOI: 10.1016/S0006-3495(00)76530-1  0.799
2000 Gorokhov A, Perera L, Darden TA, Negishi M, Pedersen LC, Pedersen LG. Heparan sulfate biosynthesis: a theoretical study of the initial sulfation step by N-deacetylase/N-sulfotransferase. Biophysical Journal. 79: 2909-17. PMID 11106599 DOI: 10.1016/S0006-3495(00)76528-3  0.795
1999 Perera L, Darden TA, Pedersen LG. Probing the structural changes in the light chain of human coagulation factor VIIa due to tissue factor association. Biophysical Journal. 77: 99-113. PMID 10388743 DOI: 10.1016/S0006-3495(99)76875-X  0.712
1999 Darden T, Perera L, Li L, Lee P. New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations Structure. 7: R55-R60. PMID 10368306 DOI: 10.1016/S0969-2126(99)80033-1  0.657
1998 Perera L, Darden TA, Pedersen LG. Trans-cis isomerization of proline 22 in bovine prothrombin fragment 1: a surprising result of structural characterization. Biochemistry. 37: 10920-7. PMID 9692984 DOI: 10.1021/Bi980263U  0.723
1998 Lim A, Saderholm MJ, Makhov AM, Kroll M, Yan Y, Perera L, Griffith JD, Erickson BW. Engineering of betabellin-15D: a 64 residue beta sheet protein that forms long narrow multimeric fibrils. Protein Science : a Publication of the Protein Society. 7: 1545-54. PMID 9684887 DOI: 10.1002/Pro.5560070708  0.374
1997 Perera L, Li L, Darden T, Monroe DM, Pedersen LG. Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method. Biophysical Journal. 73: 1847-56. PMID 9336180 DOI: 10.1016/S0006-3495(97)78215-8  0.734
1997 Yeh IC, Perera L, Berkowitz ML. Photodetachment spectra of Cl-(H2O)n clusters. Predictions and comparisons Chemical Physics Letters. 264: 31-38. DOI: 10.1016/S0009-2614(96)01322-X  0.598
1997 Perera L, Essmann U, Berkowitz ML. The role of water in the hydration force - Molecular dynamics simulations Progress in Colloid and Polymer Science. 103: 107-115. DOI: 10.1007/3-798-51084-9_12  0.589
1996 Sremaniak LS, Perera L, Berkowitz ML. Cube to cage transitions in (H2O)n (n=12, 16, and 20) Journal of Chemical Physics. 105: 3715-3721. DOI: 10.1063/1.472190  0.615
1996 Markovich G, Perera L, Berkowitz ML, Cheshnovsky O. The solvation of Cl-, Br-, and I- in acetonitrile clusters: Photoelectron spectroscopy and molecular dynamics simulations Journal of Chemical Physics. 105: 2675-2685. DOI: 10.1063/1.472131  0.603
1996 Perera L, Essmann U, Berkowitz ML. Role of water in the hydration force acting between lipid bilayers Langmuir. 12: 2625-2629. DOI: 10.1021/La9515534  0.584
1996 Sremaniak LS, Perera L, Berkowitz ML. Thermally induced structural changes in F-(H2O)11 and Cl-1(H2O)11 Clusters: Molecular dynamics computer simulations Journal of Physical Chemistry. 100: 1350-1356. DOI: 10.1021/Jp951593G  0.588
1995 Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method The Journal of Chemical Physics. 103: 8577-8593. DOI: 10.1063/1.470117  0.66
1995 Perera L, Essmann U, Berkowitz ML. Effect of the treatment of long-range forces on the dynamics of ions in aqueous solutions The Journal of Chemical Physics. 102: 450-456. DOI: 10.1063/1.469422  0.597
1995 Essmann U, Perera L, Berkowitz ML. The origin of the hydration interaction of lipid bilayers from MD simulation of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases Langmuir. 11: 4519-4531. DOI: 10.1021/La00011A056  0.588
1995 Xia X, Perera L, Essmann U, Berkowitz ML. The structure of water at platinum/water interfaces Molecular dynamics computer simulations Surface Science. 335: 401-415. DOI: 10.1016/0039-6028(95)00449-1  0.591
1994 Perera L, Berkowitz ML. Structures of Cl-(H2O)n and F -(H2O)n (n=2,3,..., 15) clusters. Molecular dynamics computer simulations The Journal of Chemical Physics. 100: 3085-3093. DOI: 10.1063/1.466450  0.611
1994 Sremaniak LS, Perera L, Berkowitz ML. Enthalpies of formation and stabilization energies of Br- (H2O)n (n=1,2, ..., 15) clusters. Comparisons between molecular dynamics computer simulations and experiment Chemical Physics Letters. 218: 377-382. DOI: 10.1016/0009-2614(93)E1493-Z  0.615
1994 Amar FG, Goyal S, Levandier DJ, Perera L, Scoles G. IR spectroscopy of solvated molecules Springer Series in Chemical Physics. 19-43.  0.658
1993 Perera L, Berkowitz ML. Erratum: Many‐body effects in molecular dynamics simulations of Na+(H2O)n and Cl−(H2O)n clusters [J. Chem. Phys. 95, 1954 (1991)] The Journal of Chemical Physics. 99: 4236-4237. DOI: 10.1063/1.466234  0.595
1993 Perera L, Berkowitz ML. Stabilization energies of Cl−, Br−, and I− ions in water clusters Journal of Chemical Physics. 99: 4222-4224. DOI: 10.1063/1.466096  0.6
1993 Vaisman II, Perera L, Berkowitz ML. Mobility of stretched water The Journal of Chemical Physics. 98: 9859-9862. DOI: 10.1063/1.464364  0.563
1993 Perera L, Berkowitz ML. Free energy profiles for Li+ and I- ions approaching the Pt(100) surface: A molecular dynamics study Journal of Physical Chemistry. 97: 13803-13806. DOI: 10.1021/J100153A059  0.588
1993 Perera L, Berkowitz ML. Ion solvation in water clusters Zeitschrift FüR Physik D Atoms, Molecules and Clusters. 26: 166-168. DOI: 10.1007/Bf01429132  0.609
1993 Perera L, Berkowitz ML. Stabilization energies of Cl-, Br-, and I- ions in water clusters The Journal of Chemical Physics. 99: 4222-4224.  0.54
1992 Perera L, Berkowitz ML. Ultrafast solvation dynamics in a Stockmayer fluid The Journal of Chemical Physics. 97: 5253-5254. DOI: 10.1063/1.463826  0.58
1992 Perera L, Berkowitz ML. Structure and dynamics of Cl−(H2O)20 clusters: The effect of the polarizability and the charge of the ion The Journal of Chemical Physics. 96: 8288-8294. DOI: 10.1063/1.462332  0.621
1992 Perera L, Berkowitz ML. Dynamics of ion solvation in a Stockmayer fluid The Journal of Chemical Physics. 96: 3092-3101. DOI: 10.1063/1.461954  0.582
1992 Perera L, Berkowitz ML. Ultrafast solvation dynamics in a Stockmayer fluid The Journal of Chemical Physics. 97: 5253-5254.  0.235
1992 Perera L, Berkowitz ML. Dynamics of ion solvation in a Stockmayer fluid The Journal of Chemical Physics. 96: 3092-3101.  0.251
1992 Perera L, Berkowitz ML. Structure and dynamics of Cl-(H2O)20 clusters: The effect of the polarizability and the charge of the ion The Journal of Chemical Physics. 96: 8288-8294.  0.316
1991 Perera L, Berkowitz ML. Many‐body effects in molecular dynamics simulations of Na+(H2O)n and Cl−(H2O)n clusters The Journal of Chemical Physics. 95: 1954-1963. DOI: 10.1063/1.460992  0.616
1991 Amar FG, Perera L. Energetics and structure in I2 -(CO2)n clusters Zeitschrift FüR Physik D Atoms, Molecules and Clusters. 20: 173-175. DOI: 10.1007/Bf01543966  0.695
1991 Perera L, Berkowitz ML. Many-body effects in molecular dynamics simulations of Na +(H2O)n and Cl-(H2O) n clusters The Journal of Chemical Physics. 95: 1954-1963.  0.291
1990 Perera L, Amar FG. Spectral shifts and structural classes in microsolutions of rare gas clusters containing a molecular chromophore The Journal of Chemical Physics. 93: 4884-4897. DOI: 10.1063/1.459686  0.711
1989 Perera L, Amar FG. Charge localization in negative ion dynamics: Effect on caging of Br 2 - in Arn and (CO2)n clusters The Journal of Chemical Physics. 90: 7354-7368. DOI: 10.1063/1.456215  0.721
1985 Thuraisingham R.A., Perera L. A compact configuration interaction wavefunction for the helium atom and the hydride ion Physics Letters A. 107: 310-313. DOI: https://doi.org/10.1016/0375-9601(85)90642-5  0.252
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