Adarsh D. Pandit, Ph.D. - Related publications

2005 University of Chicago, Chicago, IL 
studies of protein and RNA folding, function and design
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. Jacs Au. 1: 833-842. PMID 34467336 DOI: 10.1021/jacsau.1c00062   
2021 Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers. e23471. PMID 34498740 DOI: 10.1002/bip.23471   
2021 Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods in Enzymology. 656: 93-122. PMID 34325801 DOI: 10.1016/bs.mie.2021.04.009   
2021 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Featherston ER, Issertell EJ, Cotruvo JA. Probing Lanmodulin's Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage. Journal of the American Chemical Society. 143: 14287-14299. PMID 34432449 DOI: 10.1021/jacs.1c06360   
2021 Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophysical Journal. PMID 34370996 DOI: 10.1016/j.bpj.2021.08.003   
2021 Tanaka M, Kato T, Oda M. Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding. Biophysical Chemistry. 277: 106661. PMID 34388679 DOI: 10.1016/j.bpc.2021.106661   
2021 Florio G, Pugno NM, Buehler MJ, Puglisi G. A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations. Acta Biomaterialia. PMID 34303013 DOI: 10.1016/j.actbio.2021.07.032   
2021 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
2021 Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. Proceedings of Machine Learning Research. 139: 1261-1271. PMID 34423306   
2021 Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins. PMID 34312913 DOI: 10.1002/prot.26189   
2021 Cole TR, Igumenova TI. Reactivity of Thiol-Rich Zn Sites in Diacylglycerol-Sensing PKC C1 Domain Probed by NMR Spectroscopy. Frontiers in Molecular Biosciences. 8: 728711. PMID 34447788 DOI: 10.3389/fmolb.2021.728711   
2021 Michael E, Simonson T. How much can physics do for protein design? Current Opinion in Structural Biology. 72: 46-54. PMID 34461593 DOI: 10.1016/   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Ye X, Mayne L, Englander SW. A conserved strategy for structure change and energy transduction in Hsp104 and other AAA+ protein motors. The Journal of Biological Chemistry. 101066. PMID 34384781 DOI: 10.1016/j.jbc.2021.101066   
2021 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118   
2021 Olgenblum GI, Wien F, Sapir L, Harries D. β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State. The Journal of Physical Chemistry Letters. 7659-7664. PMID 34351767 DOI: 10.1021/acs.jpclett.1c02379   
2021 Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chemical Science. 12: 9528-9545. PMID 34349928 DOI: 10.1039/d1sc02520a   
2021 Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chemical Reviews. PMID 34324314 DOI: 10.1021/acs.chemrev.1c00222   
2021 Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface Salt bridges Contribute to the Extreme Thermal Stability of an FN3-like domain from a thermophilic bacterium. Proteins. PMID 34405904 DOI: 10.1002/prot.26218   
2021 Seong K, Krasileva K. Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen . Molecular Plant-Microbe Interactions : Mpmi. PMID 34415195 DOI: 10.1094/MPMI-03-21-0071-R   
2021 Van Deuren V, Yang YS, de Guillen K, Dubois C, Royer CA, Roumestand C, Barthe P. Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. Biology. 10. PMID 34356511 DOI: 10.3390/biology10070656   
2021 Ghosh B, Sengupta N. The protein hydration layer in high glucose concentration: Dynamical responses in folded and intrinsically disordered dimeric states. Biochemical and Biophysical Research Communications. 577: 124-129. PMID 34509724 DOI: 10.1016/j.bbrc.2021.09.005   
2021 Papp D, Szigyártó IC, Nordén B, Perczel A, Beke-Somfai T. Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. International Journal of Molecular Sciences. 22. PMID 34445303 DOI: 10.3390/ijms22168595   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 34338141 DOI: 10.1080/07391102.2021.1957715   
2021 Schwarz D, Georges G, Kelm S, Shi J, Vangone A, Deane CM. Co-evolutionary Distance Predictions Contain Flexibility Information. Bioinformatics (Oxford, England). PMID 34383892 DOI: 10.1093/bioinformatics/btab562   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Okuno Y, Yoo J, Schwieters CD, Best RB, Chung HS, Clore GM. Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34404723 DOI: 10.1073/pnas.2112021118   
2021 Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. Jacs Au. 1: 1217-1230. PMID 34467360 DOI: 10.1021/jacsau.1c00175   
2021 Miao Z, Wang Q, Xiao X, Kamal GM, Song L, Zhang X, Li C, Zhou X, Jiang B, Liu M. CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts. Journal of Biomolecular Nmr. PMID 34510297 DOI: 10.1007/s10858-021-00383-9   
2021 Škrbić T, Hoang TX, Giacometti A, Maritan A, Banavar JR. Spontaneous dimensional reduction and ground state degeneracy in a simple chain model. Physical Review. E. 104: L012101. PMID 34412247 DOI: 10.1103/PhysRevE.104.L012101   
2021 Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. Journal of Molecular Modeling. 27: 261. PMID 34432183 DOI: 10.1007/s00894-021-04882-2   
2021 Bergasa-Caceres F, Rabitz HA. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic. International Journal of Molecular Sciences. 22. PMID 34445324 DOI: 10.3390/ijms22168619   
2021 Wang W, Liu Q, Liu Q, Hendrickson WA. Conformational equilibria in allosteric control of Hsp70 chaperones. Molecular Cell. PMID 34453889 DOI: 10.1016/j.molcel.2021.07.039   
2021 Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods in Enzymology. 656: 1-25. PMID 34325784 DOI: 10.1016/bs.mie.2021.04.007   
2021 Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallographica. Section D, Structural Biology. 77: 1099-1115. PMID 34342282 DOI: 10.1107/S2059798321006513   
2021 Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A. The evolutionary history of topological variations in the CPA/AT transporters. Plos Computational Biology. 17: e1009278. PMID 34403419 DOI: 10.1371/journal.pcbi.1009278   
2021 Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Frontiers in Molecular Biosciences. 8: 716973. PMID 34497831 DOI: 10.3389/fmolb.2021.716973   
2021 Volkov VV, Heinz H, Perry CC. Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic-biotic interface. Physical Chemistry Chemical Physics : Pccp. PMID 34382985 DOI: 10.1039/d1cp02072b   
2021 Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2. Biomolecules. 11. PMID 34439881 DOI: 10.3390/biom11081216   
2021 Bevacqua A, Bakshi S, Xia Y. Principal component analysis of alpha-helix deformations in transmembrane proteins. Plos One. 16: e0257318. PMID 34525125 DOI: 10.1371/journal.pone.0257318   
2021 Motono C, Yanagida S, Sato M, Hirokawa T. MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. Bioinformatics (Oxford, England). PMID 34289011 DOI: 10.1093/bioinformatics/btab538   
2021 Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods in Enzymology. 656: 545-571. PMID 34325798 DOI: 10.1016/bs.mie.2021.05.008   
2021 Rumfeldt J, Kurttila M, Takala H, Ihalainen JA. The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 20: 1173-1181. PMID 34460093 DOI: 10.1007/s43630-021-00090-2   
2021 Agrawal S, Govind Kumar V, Gundampati RK, Moradi M, Kumar TKS. Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor. Scientific Reports. 11: 15579. PMID 34341408 DOI: 10.1038/s41598-021-95050-2   
2021 T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. The Journal of Physical Chemistry. B. PMID 34423989 DOI: 10.1021/acs.jpcb.1c01227   
2021 Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications. 12: 5011. PMID 34408149 DOI: 10.1038/s41467-021-25316-w   
2021 Liu YC, Yang DY, Sheu SY. Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures. International Journal of Biological Macromolecules. PMID 34536474 DOI: 10.1016/j.ijbiomac.2021.09.057