Vladislav Yakovlev - Related publications

Affiliations: 
University of Wisconsin-Milwaukee, Milwaukee, WI 
Area:
Optics Physics
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Giubertoni G, Pérez de Alba Ortíz A, Bano F, Zhang X, Linhardt RJ, Green DE, DeAngelis PL, Koenderink GH, Richter RP, Ensing B, Bakker HJ. Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca Ions. Macromolecules. 54: 1137-1146. PMID 33583956 DOI: 10.1021/acs.macromol.0c02242   
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Saha S, Bhattacharjee S, Chowdhury J. Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by calculations. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 33410370 DOI: 10.1080/07391102.2020.1870156   
2021 Ahanger IA, Parray ZA, Nasreen K, Ahmad F, Hassan MI, Islam A, Sharma A. Heparin Accelerates the Protein Aggregation via the Downhill Polymerization Mechanism: Multi-Spectroscopic Studies to Delineate the Implications on Proteinopathies. Acs Omega. 6: 2328-2339. PMID 33521471 DOI: 10.1021/acsomega.0c05638   
2021 Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. Journal of the American Chemical Society. PMID 33529004 DOI: 10.1021/jacs.0c10789   
2021 Yu HS, Modugula K, Ichihara O, Kramschuster K, Keng S, Abel R, Wang L. General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes. Journal of Chemical Theory and Computation. 17: 450-462. PMID 33372778 DOI: 10.1021/acs.jctc.0c01004   
2021 Khan FI, Song H, Hassan F, Tian J, Tang L, Lai D, Juan F. Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 253: 119572. PMID 33631627 DOI: 10.1016/j.saa.2021.119572   
2021 Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem : a European Journal of Chemical Biology. PMID 33569867 DOI: 10.1002/cbic.202000739   
2021 Sharma A, Kumari S, Goel M. Uncovering the structure-function aspects of an archaeal CsaA protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140615. PMID 33561579 DOI: 10.1016/j.bbapap.2021.140615   
2021 Dalal V, Dhankhar P, Singh V, Singh V, Rakhaminov G, Golemi-Kotra D, Kumar P. Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM. The Protein Journal. PMID 33421024 DOI: 10.1007/s10930-020-09953-6   
2021 Liu Y, Parks FC, Sheetz EG, Chen CH, Flood AH. Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion. Journal of the American Chemical Society. PMID 33596052 DOI: 10.1021/jacs.0c12562   
2021 Jankovics H, Szekér P, Tóth É, Kakasi B, Lábadi Z, Saftics A, Kalas B, Fried M, Petrik P, Vonderviszt F. Flagellin-based electrochemical sensing layer for arsenic detection in water. Scientific Reports. 11: 3497. PMID 33568718 DOI: 10.1038/s41598-021-83053-y   
2021 Kim CS, Brown AM, Grove TZ, Etzkorn FA. Designed Leucine-Rich Repeat Proteins Bind Two Muramyl Dipeptide Ligands. Protein Science : a Publication of the Protein Society. PMID 33512005 DOI: 10.1002/pro.4031   
2021 Lightwood DJ, Munro RJ, Porter J, McMillan D, Carrington B, Turner A, Scott-Tucker A, Hickford ES, Schmidt A, Fox D, Maloney A, Ceska T, Bourne T, O'Connell J, Lawson ADG. A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. Nature Communications. 12: 583. PMID 33495445 DOI: 10.1038/s41467-020-20825-6   
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 Makley LN, Johnson OT, Ghanakota P, Rauch JN, Osborn D, Wu TS, Cierpicki T, Carlson HA, Gestwicki JE. Chemical validation of a druggable site on Hsp27/HSPB1 using in silico solvent mapping and biophysical methods. Bioorganic & Medicinal Chemistry. 34: 115990. PMID 33549906 DOI: 10.1016/j.bmc.2020.115990   
2021 Mei LC, Wang YL, Wu FX, Wang F, Hao GF, Yang GF. HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Briefings in Bioinformatics. PMID 33406224 DOI: 10.1093/bib/bbaa373   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/j.abb.2020.108750   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/j.abb.2020.108750   
2021 Zhu S, Bai X, Zhu J, Li W, Wang B. Multi-spectral techniques and molecular docking to investigation of the interaction between ferulic acid and pepsin. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 251: 119442. PMID 33461141 DOI: 10.1016/j.saa.2021.119442   
2021 Shrestha R, Fajardo JE, Fiser A. Residue-based pharmacophore approaches to study protein-protein interactions. Current Opinion in Structural Biology. 67: 205-211. PMID 33486430 DOI: 10.1016/j.sbi.2020.12.016   
2021 Taneva SG, Krumova S, Bogár F, Kincses A, Stoichev S, Todinova S, Danailova A, Horváth J, Násztor Z, Kelemen L, Dér A. Insights into graphene oxide interaction with human serum albumin in isolated state and in blood plasma. International Journal of Biological Macromolecules. 175: 19-29. PMID 33508363 DOI: 10.1016/j.ijbiomac.2021.01.151   
2021 Freidel MR, Armen RS. Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. Plos One. 16: e0246181. PMID 33596235 DOI: 10.1371/journal.pone.0246181   
2021 Kheirdoosh F, Kashanian S, Khodaei MM, Sariaslani M, Falsafi M, Moghadam NH, Salehzadeh S, Pazhavand M, Kashanian M. Spectroscopic studies on the interaction of aspartame with human serum albumin. Nucleosides, Nucleotides & Nucleic Acids. 1-17. PMID 33455539 DOI: 10.1080/15257770.2021.1872792   
2021 Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry. PMID 33400518 DOI: 10.1021/acs.biochem.0c00863   
2021 He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins. PMID 33469960 DOI: 10.1002/prot.26049   
2021 Liu Y, Gong W, Yang Z, Li C. SNB-PSSM: A spatial neighbor-based PSSM used for protein-RNA binding site prediction. Journal of Molecular Recognition : Jmr. e2887. PMID 33442949 DOI: 10.1002/jmr.2887   
2021 Chundawat SPS, Nemmaru B, Hackl M, Brady SK, Hilton MA, Johnson MM, Chang S, Lang MJ, Huh H, Lee SH, Yarbrough JM, López CA, Gnanakaran S. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III. The Journal of Biological Chemistry. 100431. PMID 33610545 DOI: 10.1016/j.jbc.2021.100431   
2021 Li X, Yuan Y, Zhao R, Shao D, Bi S. Assessment on the binding characteristics of residual marbofloxacin in animal-derived food to bovine/human serum albumin by spectroscopy and molecular modeling. Luminescence : the Journal of Biological and Chemical Luminescence. PMID 33538386 DOI: 10.1002/bio.4022   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Yang M, Tang Y, Weng J, Liu Z, Wang W. The Role of Calcium in Regulating the Conformational Dynamics of d-Galactose/d-Glucose-Binding Protein Revealed by Markov State Model Analysis. Journal of Chemical Information and Modeling. PMID 33445873 DOI: 10.1021/acs.jcim.0c01119   
2021 Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short peptides as predictors for the structure of polyarginine sequences in disordered proteins. Biophysical Journal. PMID 33453267 DOI: 10.1016/j.bpj.2020.12.026   
2021 Bum-Erdene K, Liu D, Xu D, Ghozayel MK, Meroueh SO. Design and Synthesis of Fragment Derivatives with a Unique Inhibition Mechanism of the uPAR·uPA Interaction. Acs Medicinal Chemistry Letters. 12: 60-66. PMID 33488965 DOI: 10.1021/acsmedchemlett.0c00422   
2021 Moradi S, Ahmadi P, Karami C, Farhadian N, Balaei F, Ansari M, Shahlaei M. Evaluation of the effects of isoniazid and rifampin on the structure and activity of pepsin enzyme by multi spectroscopy and molecular modeling methods. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 253: 119523. PMID 33621938 DOI: 10.1016/j.saa.2021.119523   
2021 Zhu M, Song LT, Liu RR, Zhai HL, Meng YJ, Ren CL. Selective inhibition mechanism of nitroxoline to the BET family: Insight from molecular simulations. Life Sciences. 119141. PMID 33529672 DOI: 10.1016/j.lfs.2021.119141   
2021 Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. Plos Computational Biology. 17: e1008551. PMID 33481784 DOI: 10.1371/journal.pcbi.1008551   
2021 Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophysical Chemistry. 271: 106552. PMID 33581430 DOI: 10.1016/j.bpc.2021.106552   
2021 Barber NM, Lau CKY, Turner L, Watson G, Thrane S, Lusingu JPA, Lavstsen T, Higgins MK. Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein. Msphere. 6. PMID 33408232 DOI: 10.1128/mSphere.01081-20   
2021 Hays JM, Boland E, Kasson PM. Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements. The Journal of Physical Chemistry Letters. 12: 1606-1611. PMID 33596657 DOI: 10.1021/acs.jpclett.0c03623   
2021 Zhang L, Vickers TA, Sun H, Liang XH, Crooke ST. Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins. Nucleic Acids Research. PMID 33577678 DOI: 10.1093/nar/gkab078   
2021 Deng Z, Yuan B, Yang K. Cardiolipin Selectively Binds to the Interface of SemiSWEET and Regulates Its Dimerization. The Journal of Physical Chemistry Letters. 1940-1946. PMID 33591759 DOI: 10.1021/acs.jpclett.1c00022   
2021 Ha JH, Tu HC, Wilkens S, Loh SN. Loss of bound zinc facilitates amyloid fibril formation of leukocyte cell-derived chemotaxin 2 (LECT2). The Journal of Biological Chemistry. 100446. PMID 33617884 DOI: 10.1016/j.jbc.2021.100446   
2021 Castellano S, Claxton DP, Ficici E, Kusakizako T, Stix R, Zhou W, Nureki O, Mchaourab HS, Faraldo-Gómez JD. Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na in ion-coupled drug efflux. The Journal of Biological Chemistry. PMID 33402425 DOI: 10.1074/jbc.RA120.016792   
2021 Xu RG, Gauer JS, Baker SR, Slater A, Martin EM, McPherson HR, Duval C, Manfield IW, Bonna AM, Watson S, Ariëns RAS. GPVI (Glycoprotein VI) Interaction With Fibrinogen Is Mediated by Avidity and the Fibrinogen αC-Region. Arteriosclerosis, Thrombosis, and Vascular Biology. ATVBAHA120315030. PMID 33472402 DOI: 10.1161/ATVBAHA.120.315030   
2021 Palmisano VF, Gómez-Rodellar C, Pollak H, Cárdenas G, Corry B, Faraji S, Nogueira JJ. Binding of azobenzene and -diaminoazobenzene to the human voltage-gated sodium channel Na1.4. Physical Chemistry Chemical Physics : Pccp. PMID 33514952 DOI: 10.1039/d0cp06140a   
2021 Tőke O, Koprivanacz K, Radnai L, Merő B, Juhász T, Liliom K, Buday L. Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding. Cells. 10. PMID 33467043 DOI: 10.3390/cells10010173   
2021 You Y, Yang L, Chen H, Xiong L, Yang F. Effects of (-)-Epigallocatechin-3-gallate on the Functional and Structural Properties of Soybean Protein Isolate. Journal of Agricultural and Food Chemistry. PMID 33576221 DOI: 10.1021/acs.jafc.0c07337   
2021 Raj R, Agarwal N, Raghavan S, Chakraborti T, Poluri KM, Pande G, Kumar D. Epigallocatechin Gallate with Potent Anti- Activity Binds Efficiently to Its Histone-like DNA Binding Protein. Acs Omega. 6: 3548-3570. PMID 33585739 DOI: 10.1021/acsomega.0c04763   
2021 Ohgi H, Imamura H, Sumi T, Nishikawa K, Koga Y, Westh P, Morita T. Two different regimes in alcohol-induced coil-helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations. Physical Chemistry Chemical Physics : Pccp. PMID 33481971 DOI: 10.1039/d0cp05103a   
2021 Feng W, Nguyen H, Shen D, Deng H, Jiang Z, Podolnikova N, Ugarova T, Wang X. Structural Characterization of the Interaction between the αI-Domain of the Integrin Mac-1 (αβ) and the Cytokine Pleiotrophin. Biochemistry. PMID 33427449 DOI: 10.1021/acs.biochem.0c00700