Year |
Citation |
Score |
2022 |
Batra R, Loeffler TD, Chan H, Srinivasan S, Cui H, Korendovych IV, Nanda V, Palmer LC, Solomon LA, Fry HC, Sankaranarayanan SKRS. Machine learning overcomes human bias in the discovery of self-assembling peptides. Nature Chemistry. PMID 36316409 DOI: 10.1038/s41557-022-01055-3 |
0.63 |
|
2020 |
Mancini JA, Pike DH, Tyryshkin AM, Haramaty L, Wang M, Poudel S, Hecht M, Nanda V. Design of a Fe S Cluster into the Core of a De Novo 4-Helix Bundle. Biotechnology and Applied Biochemistry. PMID 32770861 DOI: 10.1002/Bab.2003 |
0.339 |
|
2020 |
Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Engineering, Design & Selection : Peds. PMID 32626892 DOI: 10.1093/Protein/Gzaa012 |
0.378 |
|
2020 |
Raanan H, Poudel S, Pike DH, Nanda V, Falkowski PG. Small protein folds at the root of an ancient metabolic network. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188785 DOI: 10.1073/Pnas.1914982117 |
0.304 |
|
2020 |
Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: Global observations and a case study of tripeptidyl-peptidase 1. The Biochemical Journal. PMID 31957806 DOI: 10.1042/Bcj20190874 |
0.325 |
|
2019 |
James JK, Nanda V. Cromparative Dynamics of Tropomyosin in Vertebrates and Invertebrates. Proteins. PMID 31390486 DOI: 10.1002/Prot.25797 |
0.354 |
|
2019 |
Mutter AC, Tyryshkin AM, Campbell IJ, Poudel S, Bennett GN, Silberg JJ, Nanda V, Falkowski PG. De novo design of symmetric ferredoxins that shuttle electrons in vivo. Proceedings of the National Academy of Sciences of the United States of America. PMID 31262814 DOI: 10.1073/Pnas.1905643116 |
0.314 |
|
2018 |
Loell K, Nanda V. Marginal protein stability drives subcellular proteome isoelectric point. Proceedings of the National Academy of Sciences of the United States of America. PMID 30385634 DOI: 10.1073/Pnas.1809098115 |
0.344 |
|
2018 |
Kim JD, Pike DH, Tyryshkin AM, Swapna GVT, Raanan H, Montelione GT, Nanda V, Falkowski PG. Minimal heterochiral de novo designed 4Fe-4S binding peptide capable of robust electron transfer. Journal of the American Chemical Society. PMID 30141918 DOI: 10.1021/Jacs.8B07553 |
0.372 |
|
2018 |
James JK, Pike DH, Khan IJ, Nanda V. Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin. Structure (London, England : 1993). PMID 29887498 DOI: 10.1016/J.Str.2018.05.002 |
0.301 |
|
2018 |
Candreva J, Chau E, Aoraha E, Nanda V, Kim JR. Hetero-assembly of a dual β-amyloid variant peptide system. Chemical Communications (Cambridge, England). PMID 29872774 DOI: 10.1039/C8Cc02724B |
0.335 |
|
2018 |
Zheng H, Lu C, Lan J, Fan S, Nanda V, Xu F. How electrostatic networks modulate specificity and stability of collagen. Proceedings of the National Academy of Sciences of the United States of America. PMID 29844169 DOI: 10.1073/Pnas.1802171115 |
0.343 |
|
2018 |
Mushnoori S, Schmidt K, Nanda V, Dutt M. Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition. Organic & Biomolecular Chemistry. PMID 29565077 DOI: 10.1039/C8Ob00130H |
0.387 |
|
2018 |
Grisham DR, Nanda V. Hydrodynamic radius coincides with the slip plane position in the electrokinetic behavior of lysozyme. Proteins. PMID 29383755 DOI: 10.1002/Prot.25469 |
0.317 |
|
2018 |
Raanan H, Pike DH, Moore EK, Falkowski PG, Nanda V. Modular origins of biological electron transfer chains. Proceedings of the National Academy of Sciences of the United States of America. PMID 29358375 DOI: 10.1073/Pnas.1714225115 |
0.303 |
|
2017 |
Nanda V, Belure SV, Shir OM. Searching for the Pareto frontier in multi-objective protein design. Biophysical Reviews. PMID 28799089 DOI: 10.1007/S12551-017-0288-0 |
0.302 |
|
2017 |
McGuinness K, Nanda V. Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions. Organic & Biomolecular Chemistry. PMID 28678287 DOI: 10.1039/C7Ob01073G |
0.39 |
|
2016 |
Drzewiecki KE, Grisham DR, Parmar AS, Nanda V, Shreiber DI. Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique. Biophysical Journal. 111: 2377-2386. PMID 27926839 DOI: 10.1016/J.Bpj.2016.10.023 |
0.319 |
|
2016 |
Maeda Y, Fang J, Ikezoe Y, Pike DH, Nanda V, Matsui H. Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides. Plos One. 11: e0153700. PMID 27116246 DOI: 10.1371/Journal.Pone.0153700 |
0.402 |
|
2016 |
Parmar AS, James JK, Grisham DR, Pike DH, Nanda V. Dissecting electrostatic contributions to folding and self-assembly using designed multicomponent peptide systems. Journal of the American Chemical Society. PMID 26966815 DOI: 10.1021/Jacs.5B10304 |
0.413 |
|
2015 |
Nanda V. Protein Design: Getting to the bottom of the TIM barrel. Nature Chemical Biology. 12: 2-3. PMID 26678608 DOI: 10.1038/Nchembio.1987 |
0.302 |
|
2015 |
Parmar AS, Xu F, Pike DH, Belure SV, Hasan NF, Drzewiecki KE, Shreiber DI, Nanda V. Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides. Biochemistry. 54: 4987-97. PMID 26225466 DOI: 10.1021/Acs.Biochem.5B00502 |
0.358 |
|
2015 |
Stapleton JA, Whitehead TA, Nanda V. Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Proceedings of the National Academy of Sciences of the United States of America. 112: 9632-7. PMID 26199411 DOI: 10.1073/Pnas.1501836112 |
0.372 |
|
2015 |
Pike DH, Nanda V. Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides. Biopolymers. 104: 360-70. PMID 25784456 DOI: 10.1002/Bip.22644 |
0.382 |
|
2015 |
McGuinness KN, Drzewiecki KE, Kopka MJ, Patel AA, Niederman RA, Shreiber DI, Nanda V. The Co-Assembly of Collagen-Mimetic Peptides and Natural Proteins Biophysical Journal. 108: 605a. DOI: 10.1016/J.Bpj.2014.11.3293 |
0.428 |
|
2014 |
McGuinness K, Khan IJ, Nanda V. Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains. Acs Nano. 8: 12514-23. PMID 25390880 DOI: 10.1021/Nn505369D |
0.426 |
|
2014 |
Parmar AS, Pike D, Nanda V. Computational design of metalloproteins. Methods in Molecular Biology (Clifton, N.J.). 1216: 233-49. PMID 25213419 DOI: 10.1007/978-1-4939-1486-9_12 |
0.314 |
|
2014 |
Huang L, Pike D, Sleat DE, Nanda V, Lobel P. Potential pitfalls and solutions for use of fluorescent fusion proteins to study the lysosome. Plos One. 9: e88893. PMID 24586430 DOI: 10.1371/Journal.Pone.0088893 |
0.338 |
|
2014 |
Senn S, Nanda V, Falkowski P, Bromberg Y. Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins. 82: 648-56. PMID 24127252 DOI: 10.1002/Prot.24442 |
0.323 |
|
2014 |
Parmar AS, Zahid S, Belure SV, Young R, Hasan N, Nanda V. Design of net-charged abc-type collagen heterotrimers. Journal of Structural Biology. 185: 163-7. PMID 23603270 DOI: 10.1016/J.Jsb.2013.04.006 |
0.331 |
|
2014 |
Parmar AS, Pike D, Nosker P, Grisham D, Hasan NF, Yin D, Chen Y, Njoku F, Lockard J, Nanda V. PH Reversible Conjugates of Graphene Oxide with Peptides and Proteins Biophysical Journal. 106: 57a. DOI: 10.1016/J.Bpj.2013.11.395 |
0.391 |
|
2014 |
Hasan NF, Parmar AS, Joshi M, Nosker P, Nanda V. Charge Crowding Promotes Self-Assembly of Collagen Hetrotrimers Biophysical Journal. 106: 680a-681a. DOI: 10.1016/J.Bpj.2013.11.3768 |
0.395 |
|
2014 |
Nosker P, Pike D, Aramini JM, Ma L, Grasso E, Montelione GT, Nanda V. Computational and Biomolecular NMR Guided Design of Peptide Theraputics for Influenza A Biophysical Journal. 106: 188a. DOI: 10.1016/J.Bpj.2013.11.1124 |
0.434 |
|
2013 |
Culik RM, Annavarapu S, Nanda V, Gai F. Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage. Chemical Physics. 422. PMID 24307748 DOI: 10.1016/J.Chemphys.2013.01.021 |
0.364 |
|
2013 |
Xu F, Khan IJ, McGuinness K, Parmar AS, Silva T, Murthy NS, Nanda V. Self-assembly of left- and right-handed molecular screws. Journal of the American Chemical Society. 135: 18762-5. PMID 24283407 DOI: 10.1021/Ja4106545 |
0.397 |
|
2013 |
Nanda V, Cristian L, Toptygin D, Brand L, Degrado WF. Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan. Chemical Physics. 422. PMID 24273370 DOI: 10.1016/J.Chemphys.2012.12.018 |
0.624 |
|
2013 |
Xu F, Silva T, Joshi M, Zahid S, Nanda V. Circular permutation directs orthogonal assembly in complex collagen peptide mixtures. The Journal of Biological Chemistry. 288: 31616-23. PMID 24043622 DOI: 10.1074/Jbc.M113.501056 |
0.41 |
|
2013 |
Nanda V, Hsieh D, Davis A. Prediction and design of outer membrane protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 1063: 183-96. PMID 23975778 DOI: 10.1007/978-1-62703-583-5_10 |
0.359 |
|
2013 |
Khan IJ, Di R, Patel P, Nanda V. Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy. Journal of Agricultural and Food Chemistry. 61: 8430-5. PMID 23926999 DOI: 10.1021/Jf401701T |
0.332 |
|
2013 |
Giddu S, Xu F, Nanda V. Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer. Proteins. 81: 386-93. PMID 23042255 DOI: 10.1002/Prot.24194 |
0.368 |
|
2013 |
McGuinness KN, Nanda V. 169 Polymorphic assembly of computationally designed hydrophobic-rich collagen peptides Journal of Biomolecular Structure and Dynamics. 31: 109-109. DOI: 10.1080/07391102.2013.786411 |
0.424 |
|
2013 |
Everson BH, French CA, Mutter AC, Nanda V, Koder RL. Hemoprotein Design using Minimal Sequence Information Biophysical Journal. 104: 661a. DOI: 10.1016/J.Bpj.2012.11.3649 |
0.369 |
|
2013 |
Parmar AS, Hasan NF, Nanda V. Structural Metal Mediated Self Assembly of Collagen Mimetic A:B:C Heterotrimer Peptides into Higher Oder Structures Biophysical Journal. 104: 48a. DOI: 10.1016/J.Bpj.2012.11.306 |
0.397 |
|
2013 |
Parmar AS, Xu F, pike D, Nanda V. Design of Structral Metal Sites in Heterospecific Collagen Peptides Biophysical Journal. 104: 400a. DOI: 10.1016/J.Bpj.2012.11.2230 |
0.365 |
|
2012 |
Kim JD, Rodriguez-Granillo A, Case DA, Nanda V, Falkowski PG. Energetic selection of topology in ferredoxins. Plos Computational Biology. 8: e1002463. PMID 22496635 DOI: 10.1371/Journal.Pcbi.1002463 |
0.404 |
|
2012 |
Grzyb J, Xu F, Nanda V, Luczkowska R, Reijerse E, Lubitz W, Noy D. Empirical and computational design of iron-sulfur cluster proteins. Biochimica Et Biophysica Acta. 1817: 1256-62. PMID 22342202 DOI: 10.1016/J.Bbabio.2012.02.001 |
0.327 |
|
2012 |
Xu F, Li J, Jain V, Tu RS, Huang Q, Nanda V. Compositional control of higher order assembly using synthetic collagen peptides. Journal of the American Chemical Society. 134: 47-50. PMID 22171825 DOI: 10.1021/Ja2077894 |
0.37 |
|
2012 |
Hsieh D, Davis A, Nanda V. A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding. Protein Science : a Publication of the Protein Society. 21: 50-62. PMID 22031179 DOI: 10.1002/Pro.758 |
0.357 |
|
2011 |
Rodriguez-Granillo A, Annavarapu S, Zhang L, Koder RL, Nanda V. Computational design of thermostabilizing D-amino acid substitutions. Journal of the American Chemical Society. 133: 18750-9. PMID 21978298 DOI: 10.1021/Ja205609C |
0.362 |
|
2011 |
Xu F, Zahid S, Silva T, Nanda V. Computational design of a collagen A:B:C-type heterotrimer. Journal of the American Chemical Society. 133: 15260-3. PMID 21902217 DOI: 10.1021/Ja205597G |
0.386 |
|
2011 |
Nanda V, Zahid S, Xu F, Levine D. Computational design of intermolecular stability and specificity in protein self-assembly. Methods in Enzymology. 487: 575-93. PMID 21187239 DOI: 10.1016/B978-0-12-381270-4.00020-2 |
0.355 |
|
2011 |
Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D. Design principles for chlorophyll-binding sites in helical proteins. Proteins. 79: 463-76. PMID 21117078 DOI: 10.1002/Prot.22895 |
0.329 |
|
2010 |
Nanda V, Koder RL. Designing artificial enzymes by intuition and computation. Nature Chemistry. 2: 15-24. PMID 21124375 DOI: 10.1038/Nchem.473 |
0.321 |
|
2010 |
Xu F, Zhang L, Koder RL, Nanda V. De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry. 49: 2307-16. PMID 20170197 DOI: 10.1021/Bi902077D |
0.428 |
|
2010 |
Grzyb J, Xu F, Weiner L, Reijerse EJ, Lubitz W, Nanda V, Noy D. De novo design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core. Biochimica Et Biophysica Acta. 1797: 406-13. PMID 20035711 DOI: 10.1016/J.Bbabio.2009.12.012 |
0.315 |
|
2009 |
Annavarapu S, Nanda V. Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. Bmc Structural Biology. 9: 61. PMID 19772623 DOI: 10.1186/1472-6807-9-61 |
0.354 |
|
2009 |
Kar K, Ibrar S, Nanda V, Getz TM, Kunapuli SP, Brodsky B. Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures. Biochemistry. 48: 7959-68. PMID 19610672 DOI: 10.1021/Bi900496M |
0.414 |
|
2008 |
McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. Journal of the American Chemical Society. 130: 11921-7. PMID 18710226 DOI: 10.1021/Ja800697G |
0.73 |
|
2008 |
Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 451: 596-9. PMID 18235504 DOI: 10.1038/Nature06528 |
0.736 |
|
2007 |
Nanda V, Andrianarijaona A, Narayanan C. The role of protein homochirality in shaping the energy landscape of folding. Protein Science : a Publication of the Protein Society. 16: 1667-75. PMID 17600146 DOI: 10.1110/Ps.072867007 |
0.369 |
|
2007 |
Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. Journal of Molecular Biology. 366: 436-48. PMID 17174324 DOI: 10.1016/J.Jmb.2006.09.020 |
0.711 |
|
2006 |
Tatko CD, Nanda V, Lear JD, Degrado WF. Polar networks control oligomeric assembly in membranes. Journal of the American Chemical Society. 128: 4170-1. PMID 16568959 DOI: 10.1021/Ja055561A |
0.527 |
|
2006 |
Nanda V, DeGrado WF. Computational design of heterochiral peptides against a helical target. Journal of the American Chemical Society. 128: 809-16. PMID 16417370 DOI: 10.1021/Ja054452T |
0.563 |
|
2006 |
Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien aMJ, DeGrado WF. Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J. Am. Chem. Soc. 2005, 127, 1346−1347]. Journal of the American Chemical Society. 128: 663-663. DOI: 10.1021/Ja059923Q |
0.481 |
|
2005 |
Cristian L, Nanda V, Lear JD, DeGrado WF. Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability. Journal of Molecular Biology. 348: 1225-33. PMID 15854657 DOI: 10.1016/J.Jmb.2005.03.053 |
0.601 |
|
2005 |
Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF. De novo design of a redox-active minimal rubredoxin mimic. Journal of the American Chemical Society. 127: 5804-5. PMID 15839675 DOI: 10.1021/Ja050553F |
0.494 |
|
2005 |
Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 59: 496-509. PMID 15789404 DOI: 10.1002/Prot.20456 |
0.532 |
|
2005 |
Nanda V, DeGrado WF. Automated use of mutagenesis data in structure prediction. Proteins. 59: 454-66. PMID 15768404 DOI: 10.1002/Prot.20382 |
0.532 |
|
2005 |
Duong-Ly KC, Nanda V, Degrado WF, Howard KP. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Science : a Publication of the Protein Society. 14: 856-61. PMID 15741338 DOI: 10.1110/Ps.041185805 |
0.568 |
|
2005 |
Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO. Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Science : a Publication of the Protein Society. 14: 1019-24. PMID 15741331 DOI: 10.1110/Ps.041110605 |
0.57 |
|
2005 |
Stouffer AL, Nanda V, Lear JD, DeGrado WF. Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. Journal of Molecular Biology. 347: 169-79. PMID 15733926 DOI: 10.1016/J.Jmb.2005.01.023 |
0.761 |
|
2005 |
Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. Journal of the American Chemical Society. 127: 1346-7. PMID 15686346 DOI: 10.1021/Ja044129A |
0.548 |
|
2005 |
Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS. A push-pull mechanism for regulating integrin function. Proceedings of the National Academy of Sciences of the United States of America. 102: 1424-9. PMID 15671157 DOI: 10.1073/Pnas.0409334102 |
0.752 |
|
2004 |
Nanda V, Degrado WF. Simulated evolution of emergent chiral structures in polyalanine. Journal of the American Chemical Society. 126: 14459-67. PMID 15521766 DOI: 10.1021/Ja0461825 |
0.52 |
|
2004 |
Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophysical Journal. 87: 3421-9. PMID 15315956 DOI: 10.1529/Biophysj.103.032839 |
0.71 |
|
2004 |
Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F. A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides. Journal of the American Chemical Society. 126: 5078-9. PMID 15099085 DOI: 10.1021/Ja032015D |
0.552 |
|
2004 |
Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes. The Journal of Biological Chemistry. 279: 26666-73. PMID 15067009 DOI: 10.1074/Jbc.M314168200 |
0.641 |
|
2004 |
Khajehpour M, Troxler T, Nanda V, Vanderkooi JM. Melittin as model system for probing interactions between proteins and cyclodextrins. Proteins. 55: 275-87. PMID 15048821 DOI: 10.1002/Prot.20036 |
0.376 |
|
2004 |
Li W, Metcalf D, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Heteromeric and Homomeric Transmembrane Domain Associations Regulate αIIbβ3 Function. Blood. 104: 329-329. DOI: 10.1182/Blood.V104.11.329.329 |
0.759 |
|
2000 |
Nanda V, Liang SM, Brand L. Hydrophobic clustering in acid-denatured IL-2 and fluorescence of a Trp NH-pi H-bond. Biochemical and Biophysical Research Communications. 279: 770-8. PMID 11162427 DOI: 10.1006/Bbrc.2000.4033 |
0.531 |
|
2000 |
Nanda V, Brand L. Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan. Proteins. 40: 112-25. PMID 10813836 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<112::Aid-Prot130>3.0.Co;2-C |
0.556 |
|
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