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Sebastian Doniach - Related publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
theoretical condensed matter physics, application of synchrotron radiation to structural studies of biological systems
Website:
http://www.stanford.edu/dept/physics/people/faculty/doniach_sebastian.html
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
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 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 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 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 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 Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chemical Reviews. PMID 34324314 DOI: 10.1021/acs.chemrev.1c00222   
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 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 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 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 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 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 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 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 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/j.sbi.2021.07.011   
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 Sharma B, Dill KA. MELD-accelerated molecular dynamics help determine amyloid fibril structures. Communications Biology. 4: 942. PMID 34354239 DOI: 10.1038/s42003-021-02461-y   
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 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 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 Park T, Woo H, Yang J, Kwon S, Won J, Seok C. Protein Oligomer Structure Prediction using GALAXY in CASP14. Proteins. PMID 34363243 DOI: 10.1002/prot.26203   
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 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 Guo M, Rosbottom I, Zhou L, Yong CW, Zhou L, Yin Q, Todorov IT, Errington E, Heng JYY. Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization. The Journal of Physical Chemistry Letters. 8416-8422. PMID 34436909 DOI: 10.1021/acs.jpclett.1c01622   
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 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
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 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   
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 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 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 Cucuzza S, Güntert P, Plückthun A, Zerbe O. An automated iterative approach for protein structure refinement using pseudocontact shifts. Journal of Biomolecular Nmr. PMID 34338940 DOI: 10.1007/s10858-021-00376-8   
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 Gao W, Shu T, Liu Q, Guo H, Ling S, Zhou L. Method of Using Raman Spectroscopy to Understand the Conformation of Fibrous Proteins. Methods in Molecular Biology (Clifton, N.J.). 2347: 229-239. PMID 34472069 DOI: 10.1007/978-1-0716-1574-4_20   
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 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 Nakamura T, Yokaichiya T, Fedorov DG. Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems. The Journal of Physical Chemistry Letters. 8757-8762. PMID 34478310 DOI: 10.1021/acs.jpclett.1c02510   
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 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 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics. e2000298. PMID 34482645 DOI: 10.1002/pmic.202000298   
2021 Liang J, Perez-Rathke A. Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units. Current Opinion in Structural Biology. 71: 200-214. PMID 34399301 DOI: 10.1016/j.sbi.2021.06.017   
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 Mule SN, Rosa-Fernandes L, Coutinho JVP, Gomes VM, Macedo-da-Silva J, Santiago VF, Quina D, de Oliveira GS, Thaysen-Andersen M, Larsen MR, Labriola L, Palmisano G. Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay. Journal of Proteomics. 248: 104355. PMID 34450331 DOI: 10.1016/j.jprot.2021.104355   
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 Kondra S, Chen F, Chen Y, Chen Y, Collette CJ, Xu W. A study of a hierarchical structure of proteins and ligand binding sites of receptors using the TSR-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures. Proteins. PMID 34392570 DOI: 10.1002/prot.26215   
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 Mir S, Ashraf S, Saeed M, Rahman AU, Ul-Haq Z. Protonation states at different pH, conformational changes and impact of glycosylation in synapsin Ia. Physical Chemistry Chemical Physics : Pccp. PMID 34318818 DOI: 10.1039/d1cp00531f