Kristoffer B. Kristensen, Ph.D. - Related publications

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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biology. 46: 102112. PMID 34537677 DOI: 10.1016/j.redox.2021.102112   
2021 Adegawa S, Yamaguchi N, Sato R. The base and root of domain II loops of Cry toxins contribute to binding to Bombyx mori ABC transporter C2. The Febs Journal. PMID 34618400 DOI: 10.1111/febs.16224   
2021 Chen YJ, Li PY, Yang CN. Molecular dynamics study of enhanced autophosphorylation by S904F mutation of the RET kinase domain. Journal of Structural Biology. 213: 107799. PMID 34563653 DOI: 10.1016/j.jsb.2021.107799   
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 Nakayoshi T, Kato K, Kurimoto E, Oda A. Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. International Journal of Molecular Sciences. 22. PMID 34576002 DOI: 10.3390/ijms22189837   
2021 Sun T, Chen Y, Wen Y, Zhu Z, Li M. PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions. Communications Biology. 4: 1311. PMID 34799678 DOI: 10.1038/s42003-021-02826-3   
2021 Zhang J, Wang K, Xue P, Chen X, Bian L. Molecular recognition and interaction between human plasminogen Kringle 5 and voltage-dependent anion channel-1 by biological specificity technologies and molecular dynamic simulation. Biophysical Chemistry. 280: 106710. PMID 34741992 DOI: 10.1016/j.bpc.2021.106710   
2021 Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. Journal of Chemical Information and Modeling. PMID 34780174 DOI: 10.1021/acs.jcim.1c00826   
2021 Liu S, Huynh T, Stauft CB, Wang TT, Luan B. Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Journal of Chemical Information and Modeling. PMID 34648284 DOI: 10.1021/acs.jcim.1c01058   
2021 Zhao X, Luo S, Huang K, Xiong D, Zhang JZH, Duan L. Targeting mechanism for SARS-CoV-2 : interaction and key groups of TMPRSS2 toward four potential drugs. Nanoscale. PMID 34787160 DOI: 10.1039/d1nr06313h   
2021 Scortecci JF, Molday LL, Curtis SB, Garces FA, Panwar P, Van Petegem F, Molday RS. Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nature Communications. 12: 5902. PMID 34625547 DOI: 10.1038/s41467-021-26161-7   
2021 Okeke CJ, Musyoka TM, Sheik Amamuddy O, Barozi V, Tastan Bishop Ö. Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance. Computational and Structural Biotechnology Journal. 19: 5647-5666. PMID 34745456 DOI: 10.1016/j.csbj.2021.10.011   
2021 Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms. Acs Omega. 6: 26354-26371. PMID 34660995 DOI: 10.1021/acsomega.1c03558   
2021 Steele TWE, Spires Z, Jones CB, Glennon RA, Dukat M, Eltit JM. Non-conserved residues dictate dopamine transporter selectivity for the potent synthetic cathinone and psychostimulant MDPV. Neuropharmacology. 108820. PMID 34619165 DOI: 10.1016/j.neuropharm.2021.108820   
2021 Skinner SP, Follmer AH, Ubbink M, Poulos TL, Houwing-Duistermaat JJ, Paci E. Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding. Biochemistry. 60: 2932-2942. PMID 34519197 DOI: 10.1021/acs.biochem.1c00406   
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 Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, et al. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. Journal of Chemical Information and Modeling. PMID 34793155 DOI: 10.1021/acs.jcim.1c00851   
2021 Evangelista W, Knapp J, Zandarashvili L, Esadze A, White MA, Gribenko AV, Lee JC. Signal Transmission in Cyclic AMP Receptor Protein for Survival in Extreme Acidic Conditions. Biochemistry. PMID 34605636 DOI: 10.1021/acs.biochem.1c00388   
2021 Díaz-Salinas MA, Li Q, Ejemel M, Yurkovetskiy L, Luban J, Shen K, Wang Y, Munro JB. Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Biorxiv : the Preprint Server For Biology. PMID 34790979 DOI: 10.1101/2021.10.29.466470   
2021 Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, et al. Discovery of SARS-CoV-2 M peptide inhibitors from modelling substrate and ligand binding. Chemical Science. 12: 13686-13703. PMID 34760153 DOI: 10.1039/d1sc03628a   
2021 Cerutti G, Guo Y, Wang P, Nair MS, Wang M, Huang Y, Yu J, Liu L, Katsamba PS, Bahna F, Reddem ER, Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Reports. 109928. PMID 34706271 DOI: 10.1016/j.celrep.2021.109928   
2021 Essegian DJ, Cunningham TA, Zerio CJ, Chapman E, Schatz J, Schürer SC. Molecular Dynamics Simulations Identify Tractable Lead-like Phenyl-Piperazine Scaffolds as eIF4A1 ATP-competitive Inhibitors. Acs Omega. 6: 24432-24443. PMID 34604625 DOI: 10.1021/acsomega.1c02805   
2021 Hu X, Pang J, Zhang J, Shen C, Chai X, Wang E, Chen H, Wang X, Duan M, Fu W, Xu L, Kang Y, Li D, Xia H, Hou T. Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2102435. PMID 34825505 DOI: 10.1002/advs.202102435   
2021 He T, Liu J, Wang JP. Development of a Dihydropteroate Synthase-Based Fluorescence Polarization Assay for Detection of Sulfonamides and Studying Its Recognition Mechanism. Journal of Agricultural and Food Chemistry. PMID 34783550 DOI: 10.1021/acs.jafc.1c05674   
2021 Harini K, Jayashree S, Tiwari V, Vishwanath S, Sowdhamini R. Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. Bioinformatics and Biology Insights. 15: 11779322211037769. PMID 34733103 DOI: 10.1177/11779322211037769   
2021 Kumar V, Parate S, Thakur G, Lee G, Ro HS, Kim Y, Kim HJ, Kim MO, Lee KW. Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations. Biomedicines. 9. PMID 34572383 DOI: 10.3390/biomedicines9091197   
2021 Murray BW, Rogers E, Zhai D, Deng W, Chen X, Sprengeler PA, Zhang X, Graber A, Reich SH, Stopatschinskaja S, Solomon B, Besse B, Drilon A. Molecular Characteristics of Repotrectinib That Enable Potent Inhibition of TRK Fusion Proteins and Resistant Mutations. Molecular Cancer Therapeutics. PMID 34625502 DOI: 10.1158/1535-7163.MCT-21-0632   
2021 Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Organic & Biomolecular Chemistry. PMID 34643629 DOI: 10.1039/d1ob01802g   
2021 Pradhan P, Margolin W, Beuria TK. Targeting the Achilles Heel of FtsZ: The Interdomain Cleft. Frontiers in Microbiology. 12: 732796. PMID 34566937 DOI: 10.3389/fmicb.2021.732796   
2021 Chen SH, Bell DR. Evolution of Thyroglobulin Loop Kinetics in EpCAM. Life (Basel, Switzerland). 11. PMID 34575064 DOI: 10.3390/life11090915   
2021 Patel MH, Dolinska MB, Sergeev YV. Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding. International Journal of Molecular Sciences. 22. PMID 34638544 DOI: 10.3390/ijms221910203   
2021 Li S, Hsieh KY, Su SC, Pintilie GD, Zhang K, Chang CI. Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. The Journal of Biological Chemistry. 101239. PMID 34563541 DOI: 10.1016/j.jbc.2021.101239   
2021 Khan MA, Kumar P, Akif M, Miyoshi H. Phosphorylation of eukaryotic initiation factor eIFiso4E enhances the binding rates to VPg of turnip mosaic virus. Plos One. 16: e0259688. PMID 34735537 DOI: 10.1371/journal.pone.0259688   
2021 Zackria AA, Pattabiraman R, Murthy TPK, Kumar SB, Mathew BB, Biju VG. Computational screening of natural compounds from R. Br. for inhibition of SARS-CoV-2 main protease. Vegetos (Bareilly, India). 1-15. PMID 34690453 DOI: 10.1007/s42535-021-00304-z   
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 Dau PT, Ishibashi H, Tuyen LH, Sakai H, Hirano M, Kim EY, Iwata H. Assessment of binding potencies of polychlorinated biphenyls and polybrominated diphenyl ethers with Baikal seal and mouse constitutive androstane receptors: Comparisons across species and congeners. The Science of the Total Environment. 150631. PMID 34592282 DOI: 10.1016/j.scitotenv.2021.150631   
2021 Foloppe N, Chen IJ. The reorganization energy of compounds upon binding to proteins, from dynamic and solvated bound and unbound states. Bioorganic & Medicinal Chemistry. 51: 116464. PMID 34798378 DOI: 10.1016/j.bmc.2021.116464   
2021 Gisriel CJ, Flesher DA, Shen G, Wang J, Ho MY, Brudvig GW, Bryant DA. Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation. The Journal of Biological Chemistry. 101408. PMID 34793839 DOI: 10.1016/j.jbc.2021.101408   
2021 Nagata T, Shinya S, Ohnuma T, Fukamizo T. Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases. Scientific Reports. 11: 2494. PMID 33510258 DOI: 10.1038/s41598-021-81903-3   
2021 Matricon P, Vo DD, Gao ZG, Kihlberg J, Jacobson KA, Carlsson J. Fragment-based design of selective GPCR ligands guided by free energy simulations. Chemical Communications (Cambridge, England). PMID 34734588 DOI: 10.1039/d1cc03202j   
2021 Alaofi AL, Shahid M. Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Biomolecules. 11. PMID 34572486 DOI: 10.3390/biom11091273   
2021 Wang P, Gao X, Zhang K, Pei Q, Xu X, Yan F, Dong J, Jing C. Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. PMID 34596645 DOI: 10.1039/d1cp02157e   
2021 Patel CN, Jani SP, Jaiswal DG, Kumar SP, Mangukia N, Parmar RM, Rawal RM, Pandya HA. Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (M) inhibitor using docking and molecular dynamics simulations. Scientific Reports. 11: 20295. PMID 34645849 DOI: 10.1038/s41598-021-99165-4   
2021 Lamichhane TR, Ghimire MP. Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function. Heliyon. 7: e08220. PMID 34693066 DOI: 10.1016/j.heliyon.2021.e08220   
2021 Wu Y, Brooks CL. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. Journal of Chemical Information and Modeling. PMID 34704754 DOI: 10.1021/acs.jcim.1c01078   
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 Farhat N, Khan AU. Repurposing drug molecule against SARS-Cov-2 (COVID-19) through molecular docking and dynamics: a quick approach to pick FDA-approved drugs. Journal of Molecular Modeling. 27: 312. PMID 34601658 DOI: 10.1007/s00894-021-04923-w   
2021 Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Computers in Biology and Medicine. 138: 104936. PMID 34655895 DOI: 10.1016/j.compbiomed.2021.104936   
2021 Yang Y, Tang T, Li X, Michel T, Ling L, Huang Z, Mulaka M, Wu Y, Gao H, Wang L, Zhou J, Meunier B, Ke H, Jiang L, Rao Y. Design, synthesis, and biological evaluation of multiple targeting antimalarials. Acta Pharmaceutica Sinica. B. 11: 2900-2913. PMID 34589403 DOI: 10.1016/j.apsb.2021.05.008   
2021 Koneru JK, Sinha S, Mondal J. Molecular Dynamics Simulations Elucidate Oligosaccharide Recognition Pathways by Galectin-3 at Atomic Resolution. The Journal of Biological Chemistry. 101271. PMID 34619151 DOI: 10.1016/j.jbc.2021.101271