Simon Olsson, Ph.D. - Related publications

Affiliations: 
University of Copenhagen, København, Denmark 
Area:
Structural Bioinformatics
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. Bmc Bioinformatics. 22: 88. PMID 33632133 DOI: 10.1186/s12859-021-04030-w   
2021 El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. The Journal of Chemical Physics. 154: 124201. PMID 33810651 DOI: 10.1063/5.0039969   
2021 Christoffer C, Chen S, Bharadwaj V, Aderinwale T, Kumar V, Hormati M, Kihara D. LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acids Research. PMID 33963854 DOI: 10.1093/nar/gkab336   
2021 Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, Gao J, Taylor EA, Sham YY. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. International Journal of Molecular Sciences. 22. PMID 33924837 DOI: 10.3390/ijms22094619   
2021 Lima I, Cino EA. Sequence similarity in 3D for comparison of protein families. Journal of Molecular Graphics & Modelling. 106: 107906. PMID 33848948 DOI: 10.1016/j.jmgm.2021.107906   
2021 Liu B, Shi H, Al-Hashimi HM. Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids. Current Opinion in Structural Biology. 70: 16-25. PMID 33836446 DOI: 10.1016/j.sbi.2021.02.007   
2021 Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL: in-depth assessment of structure quality and validation. Iucrj. 8: 238-256. PMID 33708401 DOI: 10.1107/S2052252521001159   
2021 Estrada Pabón JD, Haddox HK, Van Aken G, Pendleton IM, Eramian H, Singer JM, Schrier J. The Role of Configurational Entropy in Miniprotein Stability. The Journal of Physical Chemistry. B. PMID 33739115 DOI: 10.1021/acs.jpcb.0c09888   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Marzolf DR, Seffernick JT, Lindert S. Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. Journal of Chemical Theory and Computation. PMID 33780620 DOI: 10.1021/acs.jctc.1c00077   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Pérez-Conesa S, Keeler EG, Zhang D, Delemotte L, McDermott AE. Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel. The Journal of Chemical Physics. 154: 165102. PMID 33940802 DOI: 10.1063/5.0040649   
2021 Sahu SN, Satpathy SS, Mohanty C, Pattanayak SK. Computational study to evaluate the potency of phytochemicals in and the impact of point mutation on cyclin-dependent kinase 2-associated protein 1. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 33876720 DOI: 10.1080/07391102.2021.1914169   
2021 Waibl F, Fernández-Quintero ML, Kamenik AS, Kraml J, Hofer F, Kettenberger H, Georges G, Liedl KR. Conformational Ensembles of Antibodies Determine Their Hydrophobicity. Biophysical Journal. 120: 143-157. PMID 33220303 DOI: 10.1016/j.bpj.2020.11.010   
2021 Feng CJ, Sinitskiy A, Pande V, Tokmakoff A. Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity. The Journal of Physical Chemistry. B. PMID 33929849 DOI: 10.1021/acs.jpcb.1c00399   
2021 Li J, Xu J. Study of Real-Valued Distance Prediction for Protein Structure Prediction with Deep Learning. Bioinformatics (Oxford, England). PMID 33961022 DOI: 10.1093/bioinformatics/btab333   
2021 Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The Journal of Physical Chemistry. B. PMID 33779182 DOI: 10.1021/acs.jpcb.0c08922   
2021 Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational space sampled by domain reorientation of linear diubiquitin reflected in its binding mode for target proteins. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 33928740 DOI: 10.1002/cphc.202100187   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Hsu DJ, Leshchev D, Kosheleva I, Kohlstedt KL, Chen LX. Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations. The Journal of Chemical Physics. 154: 105101. PMID 33722011 DOI: 10.1063/5.0039194   
2021 Wang X, Alnabati E, Aderinwale TW, Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D. Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning. Nature Communications. 12: 2302. PMID 33863902 DOI: 10.1038/s41467-021-22577-3   
2021 Ploetz EA, Karunaweera S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20. Journal of Chemical Theory and Computation. PMID 33878264 DOI: 10.1021/acs.jctc.1c00076   
2021 Rhys GG, Dawson WM, Beesley JL, Martin FJO, Brady RL, Thomson AR, Woolfson DN. How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Biomacromolecules. PMID 33881308 DOI: 10.1021/acs.biomac.1c00131   
2021 Sinelnikova A, Spoel DV. NMR refinement and peptide folding using the GROMACS software. Journal of Biomolecular Nmr. PMID 33778935 DOI: 10.1007/s10858-021-00363-z   
2021 Nierzwicki Ł, Palermo G. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Frontiers in Molecular Biosciences. 8: 641208. PMID 33884260 DOI: 10.3389/fmolb.2021.641208   
2021 Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 166944. PMID 33741411 DOI: 10.1016/j.jmb.2021.166944   
2021 Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of H NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 33760611 DOI: 10.1021/acs.jpcb.1c00609   
2021 Grasso EM, Majumdar A, Wrabl JO, Frueh DP, Hilser VJ. Conserved allosteric ensembles in a disordered protein using TROSY/Anti-TROSY R-filtered spectroscopy. Biophysical Journal. PMID 33901472 DOI: 10.1016/j.bpj.2021.04.017   
2021 Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. Journal of Molecular Biology. 433: 166900. PMID 33647288 DOI: 10.1016/j.jmb.2021.166900   
2021 Kaplan AR, Olson R, Alexandrescu AT. Protein Yoga: Conformational Versatility of the Hemolysin II C-terminal Domain Detailed by NMR Structures for Multiple States. Protein Science : a Publication of the Protein Society. PMID 33733504 DOI: 10.1002/pro.4066   
2021 Hu LB, Hu XQ, Zhang Q, You QD, Jiang ZY. An affinity prediction approach for the ligand of E3 ligase Cbl-b and an insight into substrate binding pattern. Bioorganic & Medicinal Chemistry. 38: 116130. PMID 33848699 DOI: 10.1016/j.bmc.2021.116130   
2021 Blaber M. Cooperative hydrophobic core interactions in the β-trefoil architecture. Protein Science : a Publication of the Protein Society. PMID 33686691 DOI: 10.1002/pro.4059   
2021 Rathore I, Mishra V, Bhaumik P. Advancements in macromolecular crystallography: from past to present. Emerging Topics in Life Sciences. PMID 33969867 DOI: 10.1042/ETLS20200316   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Ahmed J, Kumar K, Sharma K, Fontes CMGA, Goyal A. Computational and SAXS-based structure insights of pectin acetyl esterase (Pae12B) of family 12 carbohydrate esterase from ATCC 27405. Journal of Biomolecular Structure & Dynamics. 1-18. PMID 33860720 DOI: 10.1080/07391102.2021.1911858   
2021 Ahmed J, Kumar K, Sharma K, Fontes CMGA, Goyal A. Computational and SAXS-based structure insights of pectin acetyl esterase (Pae12B) of family 12 carbohydrate esterase from ATCC 27405. Journal of Biomolecular Structure & Dynamics. 1-18. PMID 33860720 DOI: 10.1080/07391102.2021.1911858   
2021 Rao AG, Wiebeler C, Sen S, Cerutti DS, Schapiro I. Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2. Physical Chemistry Chemical Physics : Pccp. 23: 7359-7367. PMID 33876095 DOI: 10.1039/d0cp05314g   
2021 Forouzesh N, Mishra N. An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor. Molecules (Basel, Switzerland). 26. PMID 33923909 DOI: 10.3390/molecules26082383   
2021 Mitra A, Sarkar A, Szabó MR, Borics A. Correlated Motions of Conserved Polar Motifs Lay out a Plausible Mechanism of G Protein-Coupled Receptor Activation. Biomolecules. 11. PMID 33946214 DOI: 10.3390/biom11050670   
2021 Hett T, Zbik T, Mukherjee S, Matsuoka H, Bönigk W, Klose D, Rouillon C, Brenner N, Peuker S, Klement R, Steinhoff HJ, Grubmüller H, Seifert R, Schiemann O, Kaupp UB. Spatiotemporal Resolution of Conformational Changes in Biomolecules by Combining Pulsed Electron-Electron Double Resonance Spectroscopy with Microsecond Freeze-Hyperquenching. Journal of the American Chemical Society. PMID 33905249 DOI: 10.1021/jacs.1c01081   
2021 Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. The Journal of Physical Chemistry. B. PMID 33818099 DOI: 10.1021/acs.jpcb.1c00972   
2021 Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. Journal of the American Chemical Society. PMID 33661624 DOI: 10.1021/jacs.0c11806   
2021 Dawson WM, Lang EJM, Rhys GG, Shelley KL, Williams C, Brady RL, Crump MP, Mulholland AJ, Woolfson DN. Structural resolution of switchable states of a de novo peptide assembly. Nature Communications. 12: 1530. PMID 33750792 DOI: 10.1038/s41467-021-21851-8   
2021 Wang L, Cao C, Zuo S. Protein secondary structure assignment using pc-polyline and convolutional neural network. Proteins. PMID 33780034 DOI: 10.1002/prot.26079   
2021 Assaiya A, Burada AP, Dhingra S, Kumar J. An overview of the recent advances in cryo-electron microscopy for life sciences. Emerging Topics in Life Sciences. PMID 33760078 DOI: 10.1042/ETLS20200295   
2021 Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. The Journal of Physical Chemistry. B. PMID 33826319 DOI: 10.1021/acs.jpcb.0c10992   
2021 Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. The Journal of Biological Chemistry. 100556. PMID 33744289 DOI: 10.1016/j.jbc.2021.100556