William Clemons, Ph.D. - Related publications

Chemistry and Chemical Engineering California Institute of Technology, Pasadena, CA 
X-ray crystallography
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure (London, England : 1993). PMID 34587504 DOI: 10.1016/j.str.2021.09.002   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis. 161: 105236. PMID 34648928 DOI: 10.1016/j.micpath.2021.105236   
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. The Journal of Physical Chemistry. B. PMID 34748336 DOI: 10.1021/acs.jpcb.1c05820   
2021 Xu YC, ShangGuan TJ, Ding XM, Cheung NJ. Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. Scientific Reports. 11: 21033. PMID 34702851 DOI: 10.1038/s41598-021-00477-2   
2021 Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Communications Biology. 4: 1240. PMID 34716407 DOI: 10.1038/s42003-021-02766-y   
2021 Cui H, Müller AU, Leibundgut M, Tian J, Ban N, Weber-Ban E. Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Nature Communications. 12: 6635. PMID 34789727 DOI: 10.1038/s41467-021-26848-x   
2021 Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chemical Science. 12: 13492-13505. PMID 34777769 DOI: 10.1039/d1sc02775a   
2021 Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B. Designer proteins that competitively inhibit Gα by targeting its effector site. The Journal of Biological Chemistry. 101348. PMID 34715131 DOI: 10.1016/j.jbc.2021.101348   
2021 Patel VR, Salinas AM, Qi D, Gupta S, Sidote DJ, Goldschen-Ohm MP. Single-molecule imaging with cell-derived nanovesicles reveals early binding dynamics at a cyclic nucleotide-gated ion channel. Nature Communications. 12: 6459. PMID 34753946 DOI: 10.1038/s41467-021-26816-5   
2021 James JK, Nanda V. A Folding Insulator Defines Cryptic Domains in Tropomyosin. Journal of Molecular Biology. 433: 167281. PMID 34606830 DOI: 10.1016/j.jmb.2021.167281   
2021 Adams M, Sharma R, Colby T, Weis F, Matic I, Bhogaraju S. Structural basis for protein glutamylation by the Legionella pseudokinase SidJ. Nature Communications. 12: 6174. PMID 34702826 DOI: 10.1038/s41467-021-26429-y   
2021 Jang H, Lee C, Hwang Y, Lee SJ. Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences. Dalton Transactions (Cambridge, England : 2003). PMID 34806716 DOI: 10.1039/d1dt03501k   
2021 Yan XF, Yang C, Wang M, Yong Y, Deng Y, Gao YG. Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum sensing system in Burkholderia cenocepacia. Febs Letters. PMID 34837384 DOI: 10.1002/1873-3468.14244   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Vankayala SL, Warrensford LC, Pittman AR, Pollard BC, Kearns FL, Larkin JD, Woodcock HL. CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. Journal of Computational Chemistry. PMID 34741467 DOI: 10.1002/jcc.26759   
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 Goult BT, Brown NH, Schwartz MA. Talin in mechanotransduction and mechanomemory at a glance. Journal of Cell Science. 134. PMID 34708856 DOI: 10.1242/jcs.258749   
2021 Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society. PMID 34757725 DOI: 10.1021/jacs.1c10588   
2021 Anchal, Kaushik V, Goel M. Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea. Frontiers in Microbiology. 12: 751049. PMID 34691003 DOI: 10.3389/fmicb.2021.751049   
2021 Plessa E, Chu LP, Chan SHS, Thomas OL, Cassaignau AME, Waudby CA, Christodoulou J, Cabrita LD. Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein. Nature Communications. 12: 6447. PMID 34750347 DOI: 10.1038/s41467-021-26531-1   
2021 Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, et al. Structure, function and pharmacology of human itch receptor complexes. Nature. PMID 34789875 DOI: 10.1038/s41586-021-04077-y   
2021 Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj. 8: 954-962. PMID 34804547 DOI: 10.1107/S2052252521009386   
2021 Rübbelke M, Hamilton J, Binder F, Bauer M, King J, Nar H, Zeeb M. Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain. Journal of Medicinal Chemistry. PMID 34672548 DOI: 10.1021/acs.jmedchem.1c00686   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Juanes-Gusano D, Santos M, Reboto V, Alonso M, Rodríguez-Cabello JC. Self-assembling systems comprising intrinsically disordered protein polymers like elastin-like recombinamers. Journal of Peptide Science : An Official Publication of the European Peptide Society. e3362. PMID 34545666 DOI: 10.1002/psc.3362   
2021 Correia VG, Trovão F, Pinheiro BA, Brás JLA, Silva LM, Nunes C, Coimbra MA, Liu Y, Feizi T, Fontes CMGA, Mulloy B, Chai W, Carvalho AL, Palma AS. Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Microbiology Spectrum. e0182621. PMID 34817219 DOI: 10.1128/Spectrum.01826-21   
2021 Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Frontiers in Molecular Biosciences. 8: 707661. PMID 34532343 DOI: 10.3389/fmolb.2021.707661   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Modi V, Dunbrack RL. Kincore: a web resource for structural classification of protein kinases and their inhibitors. Nucleic Acids Research. PMID 34643709 DOI: 10.1093/nar/gkab920   
2021 Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ. The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34548394 DOI: 10.1073/pnas.2023898118   
2021 Baucom DR, Furr M, Kumar VG, Okoto P, Losey JL, Henry RL, Moradi M, Suresh Kumar TK, Heyes CD. Transient Local Secondary Structure in the Intrinsically Disordered C-Term of the Albino3 Insertase. Biophysical Journal. PMID 34662559 DOI: 10.1016/j.bpj.2021.10.013   
2021 Kim DG, Baek I, Lee Y, Kim H, Kim JY, Bang G, Kim S, Yoon HJ, Han BW, Suh SW, Kim HS. Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Acta Crystallographica. Section D, Structural Biology. 77: 1460-1474. PMID 34726173 DOI: 10.1107/S2059798321010068   
2021 Huang Q, Ng EY, Li Q, Kang C.  H,  N and  C resonance assignments of the Q61H mutant of human KRAS bound to GDP. Biomolecular Nmr Assignments. PMID 34787842 DOI: 10.1007/s12104-021-10058-z   
2021 Fuzo CA, de Araujo LFL, Pontes RS, Évora PM, Stabeli RG. Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation. Journal of Biomolecular Structure & Dynamics. 39: 1082-1092. PMID 32090677 DOI: 10.1080/07391102.2020.1728385   
2021 Heltberg ML, Miné-Hattab J, Taddei A, Walczak AM, Mora T. Physical observables to determine the nature of membrane-less cellular sub-compartments. Elife. 10. PMID 34677123 DOI: 10.7554/eLife.69181   
2021 Conseil G, Cole SPC. The First Cytoplasmic Loop in the Core Structure of the ABCC1 (Multidrug Resistance Protein 1; MRP1) Transporter Contains Multiple Amino Acids Essential for Its Expression. International Journal of Molecular Sciences. 22. PMID 34575890 DOI: 10.3390/ijms22189710   
2021 Wang Z, Zheng L, Liu Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells. Frontiers in Chemistry. 9: 753002. PMID 34778208 DOI: 10.3389/fchem.2021.753002   
2021 Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, et al. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. The Isme Journal. PMID 34556817 DOI: 10.1038/s41396-021-01113-7   
2021 Wofford HA, Myers-Dean J, Vogel BA, Alamo KAE, Longshore-Neate FA, Jagodzinski F, Amacher JF. Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in PDZ Domains Using Human PDZ Data. Molecules (Basel, Switzerland). 26. PMID 34641578 DOI: 10.3390/molecules26196034   
2021 Byeon IL, Calero G, Wu Y, Byeon CH, Jung J, DeLucia M, Zhou X, Weiss S, Ahn J, Hao C, Skowronski J, Gronenborn AM. Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A. Nature Communications. 12: 6864. PMID 34824204 DOI: 10.1038/s41467-021-27009-w   
2021 Mikkelsen MD, Cao HTT, Roret T, Rhein-Knudsen N, Holck J, Tran VTT, Nguyen TT, Tran VHN, Lezyk MJ, Muschiol J, Pham TD, Czjzek M, Meyer AS. A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. Scientific Reports. 11: 19523. PMID 34593864 DOI: 10.1038/s41598-021-98588-3   
2021 Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science. 12: 11275-11293. PMID 34667539 DOI: 10.1039/d1sc02751d   
2021 Vongsouthi V, Whitfield JH, Unichenko P, Mitchell JA, Breithausen B, Khersonsky O, Kremers L, Janovjak H, Monai H, Hirase H, Fleishman SJ, Henneberger C, Jackson CJ. A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine. Acs Sensors. 6: 4193-4205. PMID 34783546 DOI: 10.1021/acssensors.1c01803   
2021 Sanejouand YH. Normal-mode driven exploration of protein domain motions. Journal of Computational Chemistry. 42: 2250-2257. PMID 34599620 DOI: 10.1002/jcc.26755