Yoshiaki Z. Ohkubo, Ph.D. - Related publications

Affiliations: 
2000 University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Pharmaceutical Chemistry, General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Liang S, Li Z, Zhan J, Zhou Y. De Novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinformatics (Oxford, England). PMID 34406339 DOI: 10.1093/bioinformatics/btab598   
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 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 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 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 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 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 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 Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 10. PMID 34623258 DOI: 10.7554/eLife.70236   
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 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 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 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 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 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 Taujale R, Zhou Z, Yeung W, Moremen KW, Li S, Kannan N. Mapping the glycosyltransferase fold landscape using interpretable deep learning. Nature Communications. 12: 5656. PMID 34580305 DOI: 10.1038/s41467-021-25975-9   
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 Konovalov KA, Unarta IC, Cao S, Goonetilleke EC, Huang X. Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning. Jacs Au. 1: 1330-1341. PMID 34604842 DOI: 10.1021/jacsau.1c00254   
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 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 Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XIV. Proteins. PMID 34533838 DOI: 10.1002/prot.26237   
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 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 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
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 Guo L, Dutton OJ, Kucukdisli M, Davy M, Wagnières O, Butts CP, Myers EL, Aggarwal VK. Conformationally Controlled Linear and Helical Hydrocarbons Bearing Extended Side Chains. Journal of the American Chemical Society. PMID 34590479 DOI: 10.1021/jacs.1c07778   
2021 Murata H, Imakawa H, Koga N, Chikenji G. The register shift rules for βαβ-motifs for de novo protein design. Plos One. 16: e0256895. PMID 34460870 DOI: 10.1371/journal.pone.0256895   
2021 Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V-V Interface Dynamics. Frontiers in Immunology. 12: 675655. PMID 34447370 DOI: 10.3389/fimmu.2021.675655   
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 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 Skolnick J, Gao M, Zhou H, Singh S. AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. Journal of Chemical Information and Modeling. PMID 34586808 DOI: 10.1021/acs.jcim.1c01114   
2021 Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J. Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins. PMID 34462960 DOI: 10.1002/prot.26231   
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 Barozet A, Molloy K, Vaisset M, Zanon C, Fauret P, Siméon T, Cortés J. MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations. Bioinformatics (Oxford, England). PMID 34432000 DOI: 10.1093/bioinformatics/btab584   
2021 Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg and ADP:Mg using the polarizable force field AMOEBA. Molecular Simulation. 47: 439-448. PMID 34421214 DOI: 10.1080/08927022.2020.1725003   
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 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 Lv TM, Chen DL, Liang JJ, Bai M, Lin B, Huang XX, Ma GX, Song SJ. Structural Revisions of Two Highly Aromatic Naphthoquinone-Derived Dimers Based on NMR Analysis, Computer-Assisted Structure Elucidation Methods, and Computations. Organic Letters. PMID 34436914 DOI: 10.1021/acs.orglett.1c02626   
2021 Ruff KM, Pappu RV. AlphaFold and implications for intrinsically disordered proteins. Journal of Molecular Biology. 167208. PMID 34418423 DOI: 10.1016/j.jmb.2021.167208   
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 Yang J, Zhang P, Cheng WX, Lu Y, Gang W, Ren G. Exposing Structural Variations in SARS-CoV-2 Evolution. Research Square. PMID 34545355 DOI: 10.21203/rs.3.rs-800496/v1   
2021 Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure (London, England : 1993). PMID 34331857 DOI: 10.1016/j.str.2021.07.001   
2021 Huang S, Mei H, Lu L, Kuang Z, Heng Y, Xu L, Liang X, Qiu M, Pan X. Conformational transitions of caspase-6 in substrate-induced activation process explored by perturbation-response scanning combined with targeted molecular dynamics. Computational and Structural Biotechnology Journal. 19: 4156-4164. PMID 34527189 DOI: 10.1016/j.csbj.2021.07.017   
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 Mayerthaler F, Feldberg AL, Alfermann J, Sun X, Steinchen W, Yang H, Mootz HD. Intermediary conformations linked to the directionality of the aminoacylation pathway of nonribosomal peptide synthetases. Rsc Chemical Biology. 2: 843-854. PMID 34458813 DOI: 10.1039/d0cb00220h   
2021 Rajale T, Miner JC, Michalczyk R, Phipps ML, Schmidt JG, Gilbertson RD, Williams RF, Strauss CEM, Martinez JS. Conformational control sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling. Chemical Communications (Cambridge, England). PMID 34498621 DOI: 10.1039/d1cc01992a   
2021 Parkman JA, Barksdale CA, Michaelis DJ. CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations. Journal of Computational Chemistry. PMID 34411332 DOI: 10.1002/jcc.26729   
2021 de C Bittencourt DM, Oliveira PF, Souto BM, de Freitas SM, Silva LP, Murad AM, Michalczechen-Lacerda VA, Lewis RV, Rech EL. Molecular Dynamics of Synthetic Flagelliform Silk Fiber Assembly. Macromolecular Materials and Engineering. 306. PMID 34539237 DOI: 10.1002/mame.202000530   
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 Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Science : a Publication of the Protein Society. PMID 34523753 DOI: 10.1002/pro.4184