Christopher W.V. Hogue - Related publications

Affiliations: 
1997-2008 Biochemistry University of Toronto, Toronto, ON, Canada 
 2007-2013 Biol. Sciences National University of Singapore, Singapore, Singapore 
Website:
http://bioimplement.blogspot.com/
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 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 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Peterson TA, Piper RC. Deconvolution of Multiple Rab Binding Domains Using the Batch Yeast 2-Hybrid Method DEEPN. Methods in Molecular Biology (Clifton, N.J.). 2293: 117-141. PMID 34453714 DOI: 10.1007/978-1-0716-1346-7_9   
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 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
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 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 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 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 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 Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, Shifman JM. Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein-Protein Complexes. Journal of the American Chemical Society. PMID 34609866 DOI: 10.1021/jacs.1c08707   
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 Kumar A, Jernigan RL. Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations. Frontiers in Molecular Biosciences. 8: 733148. PMID 34540902 DOI: 10.3389/fmolb.2021.733148   
2021 Xiao T, Sun L, Zhang M, Li Z, Haura EB, Schonbrunn E, Ji H. Synthesis and Structural Characterization of a Monocarboxylic Inhibitor for GRB2 SH2 Domain. Bioorganic & Medicinal Chemistry Letters. 128354. PMID 34506932 DOI: 10.1016/j.bmcl.2021.128354   
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 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 Sun L, Fu T, Zhao D, Fan H, Zhong S. Divide-and-link peptide docking: a fragment-based peptide docking protocol. Physical Chemistry Chemical Physics : Pccp. PMID 34596658 DOI: 10.1039/d1cp02098f   
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 Gubensäk N, Schrank E, Hartlmüller C, Göbl C, Falsone FS, Becker W, Wagner GE, Pulido S, Meyer NH, Pavkov-Keller T, Madl T, Reidl J, Zangger K. Structural and DNA binding properties of the cytoplasmic domain of Vibrio cholerae transcription factor ToxR. The Journal of Biological Chemistry. 101167. PMID 34487759 DOI: 10.1016/j.jbc.2021.101167   
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 Braun L, Schoen I, Vogel V. PIP-induced membrane binding of the Vinculin tail competes with its other binding partners. Biophysical Journal. PMID 34411575 DOI: 10.1016/j.bpj.2021.08.018   
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 Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. International Journal of Molecular Sciences. 22. PMID 33498210 DOI: 10.3390/ijms22030997   
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 Liu W, Li C, Shan J, Wang Y, Chen G. Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration. Royal Society Open Science. 8: 210160. PMID 34457335 DOI: 10.1098/rsos.210160   
2021 Zhu Y, Ye F, Zhou Z, Liu W, Liang Z, Hu G. Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions. Molecules (Basel, Switzerland). 26. PMID 34500587 DOI: 10.3390/molecules26175153   
2021 Ali MS, Rehman MT, Al-Lohedan HA, AlAjmi MF. Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 34488560 DOI: 10.1080/07391102.2021.1971560   
2021 Padhi AK, Kumar A, Haruna KI, Sato H, Tamura H, Nagatoishi S, Tsumoto K, Yamaguchi A, Iraha F, Takahashi M, Sakamoto K, Zhang KYJ. An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Briefings in Bioinformatics. PMID 34415295 DOI: 10.1093/bib/bbab338   
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 Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophysical Journal. PMID 34555362 DOI: 10.1016/j.bpj.2021.09.026   
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 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
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 Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W. Structures of heat shock factor trimers bound to DNA. Iscience. 24: 102951. PMID 34458700 DOI: 10.1016/j.isci.2021.102951   
2021 Yeggoni DP, Dubey S, Mohammad YZ, Rachamallu A, Subramanyam R. Elucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34463217 DOI: 10.1080/07391102.2021.1968498   
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 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 Sahoo S, Dehury B, Narang PK, Raina V, Misra N, Suar M. Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an study to vitalize the development of optimum engineered strains with high lipid productivity. Journal of Biomolecular Structure & Dynamics. 1-19. PMID 34415234 DOI: 10.1080/07391102.2021.1967194   
2021 Lauer J, Zerial M. Profiling Structural Alterations During Rab5 Nucleotide Exchange by HDX-MS. Methods in Molecular Biology (Clifton, N.J.). 2293: 69-89. PMID 34453711 DOI: 10.1007/978-1-0716-1346-7_6   
2021 VanSchouwen B, Boulton S, Melacini G. Mutual Protein-Ligand Conformational Selection Drives cGMP vs. cAMP Selectivity in Protein Kinase G. Journal of Molecular Biology. 433: 167202. PMID 34400180 DOI: 10.1016/j.jmb.2021.167202   
2021 Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallographica. Section D, Structural Biology. 77: 1168-1182. PMID 34473087 DOI: 10.1107/S2059798321008196   
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 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 Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen HY, Huang S. Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap. Angewandte Chemie (International Ed. in English). PMID 34449124 DOI: 10.1002/anie.202110545   
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 Capponi S, Wang S, Navarro EJ, Bianco S. AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations. The European Physical Journal. E, Soft Matter. 44: 123. PMID 34613523 DOI: 10.1140/epje/s10189-021-00119-5   
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 Cao Y, Choi YK, Frank M, Woo H, Park SJ, Yeom MS, Seok C, Im W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Journal of Chemical Theory and Computation. PMID 34529436 DOI: 10.1021/acs.jctc.1c00552   
2021 Hwang J, Park SH, Lee CW, Do H, Shin SC, Kim HW, Lee SG, Park HH, Kwon S, Lee JH. Crystal structure of a MarR family protein from the psychrophilic bacterium sp. TG-14 in complex with a lipid-like molecule. Iucrj. 8: 842-852. PMID 34584745 DOI: 10.1107/S2052252521005704   
2021 Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. Plos One. 16: e0257206. PMID 34506566 DOI: 10.1371/journal.pone.0257206