Avadhesha Surolia - Related publications

Affiliations: 
Molecular Biophysics Unit Indian Institute of Science Bangalore 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Yin Z. Virtual Screening by 2-D Fingerprints, Shape and Docking for Discovering New Chemotypes of Activator Protein-1 Inhibitors. Journal of Biomolecular Structure & Dynamics. 1-12. PMID 32223539 DOI: 10.1080/07391102.2020.1749130   
2020 Chen S, Gong X, Tan H, Liu Y, He L, Ouyang J. Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches. Talanta. 211: 120762. PMID 32070628 DOI: 10.1016/j.talanta.2020.120762   
2020 Longo LM, Petrović D, Kamerlin SCL, Tawfik DS. Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proceedings of the National Academy of Sciences of the United States of America. PMID 32079722 DOI: 10.1073/pnas.1911742117   
2020 Moussu S, Broyart C, Santos-Fernandez G, Augustin S, Wehrle S, Grossniklaus U, Santiago J. Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth. Proceedings of the National Academy of Sciences of the United States of America. PMID 32165538 DOI: 10.1073/pnas.2000100117   
2020 Dong M, Harikumar KG, Raval SR, Milburn JE, Clark C, Alcala-Torano R, Mobarec JC, Reynolds CA, Ghirlanda G, Christopoulos A, Wootten D, Sexton PM, Miller LJ. Rational development of a high-affinity secretin receptor antagonist. Biochemical Pharmacology. 113929. PMID 32217097 DOI: 10.1016/j.bcp.2020.113929   
2020 Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. The Journal of Physical Chemistry. B. PMID 32097002 DOI: 10.1021/acs.jpcb.0c00167   
2020 Gaddi GM, Gisonno RA, Rosú SA, Curto LM, Prieto ED, Schinella GR, Finarelli GS, Cortez MF, Bauzá L, Elías EE, Ramella NA, Tricerri MA. Structural analysis of a natural apolipoprotein A-I variant (L60R) associated with amyloidosis. Archives of Biochemistry and Biophysics. 108347. PMID 32194045 DOI: 10.1016/j.abb.2020.108347   
2020 Gaddi GM, Gisonno RA, Rosú SA, Curto LM, Prieto ED, Schinella GR, Finarelli GS, Cortez MF, Bauzá L, Elías EE, Ramella NA, Tricerri MA. Structural analysis of a natural apolipoprotein A-I variant (L60R) associated with amyloidosis. Archives of Biochemistry and Biophysics. 108347. PMID 32194045 DOI: 10.1016/j.abb.2020.108347   
2020 Lim NM, Osato M, Warren GL, Mobley DL. Fragment pose prediction using non-equilibrium candidate Monte Carlo and molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 32167763 DOI: 10.1021/acs.jctc.9b01096   
2020 Su H, Zou Y, Chen G, Dou H, Xie H, Yuan X, Zhang X, Zhang N, Li M, Xu Y. Exploration of Fragment Binding Poses Leading to Efficient Discovery of Highly Potent and Orally Effective Inhibitors of FABP4 for Anti-inflammation. Journal of Medicinal Chemistry. PMID 32202425 DOI: 10.1021/acs.jmedchem.9b02107   
2020 Zhao B, Payne WG, Sai J, Lu Z, Olejniczak ET, Fesik SW. Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex. Biochemistry. PMID 32032490 DOI: 10.1021/acs.biochem.9b01073   
2020 Nguyen LH, Tran TT, Truong LTN, Mai HH, Nguyen TT. Overcharging of zinc ion in the structure of zinc-finger protein is needed for DNA binding stability. Biochemistry. PMID 32043865 DOI: 10.1021/acs.biochem.9b01055   
2020 Jin Z, Wang Y, Yu XF, Tan QQ, Liang SS, Li T, Zhang H, Shaw PC, Wang J, Hu C. Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation. Computational Biology and Chemistry. 85: 107241. PMID 32120300 DOI: 10.1016/j.compbiolchem.2020.107241   
2020 Bonarek P, Loch JI, Tworzydło M, Cooper DR, Milto K, Wróbel P, Kurpiewska K, Lewiński K. Structure-based design approach to rational site-directed mutagenesis of β-lactoglobulin. Journal of Structural Biology. 107493. PMID 32169624 DOI: 10.1016/j.jsb.2020.107493   
2020 Konar M, Sahoo H. Tyrosine mediated conformational change in bone morphogenetic protein - 2: Biophysical implications of protein - Phytoestrogen interaction. International Journal of Biological Macromolecules. PMID 32061704 DOI: 10.1016/j.ijbiomac.2020.02.113   
2020 Gose T, Shafi T, Fukuda Y, Das S, Wang Y, Allcock A, Gavan McHarg A, Lynch J, Chen T, Tamai I, Shelat A, Ford RC, Schuetz JD. ABCG2 requires a single aromatic amino acid to "clamp" substrates and inhibitors into the binding pocket. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 32067270 DOI: 10.1096/fj.201902338RR   
2020 Kumar A, Rai S, Rathi E, Agarwal P, Kini SG. Pharmacophore-guided fragment-based design of novel mammalian target of rapamycin inhibitors: Extra precision docking, fingerprint-based 2D and atom-based 3D-QSAR modelling. Journal of Biomolecular Structure & Dynamics. 1-29. PMID 32037974 DOI: 10.1080/07391102.2020.1726816   
2020 Gunnell EA, Al-Noori A, Muhsen U, Davies CC, Dowden J, Dreveny I. Structural and biochemical evaluation of bisubstrate inhibitors of protein arginine N-methyltransferases PRMT1 and CARM1 (PRMT4). The Biochemical Journal. PMID 32011657 DOI: 10.1042/BCJ20190826   
2020 Wu Y, Lou L, Xie ZR. A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. Frontiers in Chemistry. 8: 81. PMID 32117898 DOI: 10.3389/fchem.2020.00081   
2020 Vahidi S, Ripstein ZA, Juravsky JB, Rennella E, Goldberg AL, Mittermaier AK, Rubinstein JL, Kay LE. An allosteric switch regulates ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR. Proceedings of the National Academy of Sciences of the United States of America. PMID 32123115 DOI: 10.1073/pnas.1921630117   
2020 Rashid S, Lee BL, Wajda B, Spyracopoulos L. Nucleotide Binding and Active Site Gate Dynamics for the Hsp90 Chaperone ATPase Domain from Benchtop and High Field F NMR Spectroscopy. The Journal of Physical Chemistry. B. PMID 32212608 DOI: 10.1021/acs.jpcb.0c00626   
2020 Dietrich C, Li de la Sierra-Gallay I, Masi M, Girard E, Dautin N, Constantinesco-Becker F, Tropis M, Daffé M, van Tilbeurgh H, Bayan N. The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability. Molecular Microbiology. PMID 32073722 DOI: 10.1111/mmi.14492   
2020 Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P. Selectively disrupting mA-dependent protein-RNA interactions with fragments. Acs Chemical Biology. PMID 32101404 DOI: 10.1021/acschembio.9b00894   
2020 Bresso E, Furlan A, Noel P, Leroux V, Maina F, Dono R, Maigret B. Large-Scale Virtual Screening Against the MET Kinase Domain Identifies a New Putative Inhibitor Type. Molecules (Basel, Switzerland). 25. PMID 32093126 DOI: 10.3390/molecules25040938   
2020 Anighoro A. Underappreciated Chemical Interactions in Protein-Ligand Complexes. Methods in Molecular Biology (Clifton, N.J.). 2114: 75-86. PMID 32016887 DOI: 10.1007/978-1-0716-0282-9_5   
2020 Tran DP, Kitao A. Kinetic selection and relaxation of the Intrinsically Disordered Region of a Protein upon Binding. Journal of Chemical Theory and Computation. PMID 32192337 DOI: 10.1021/acs.jctc.9b01203   
2020 Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dells Eacute N A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. Journal of the American Chemical Society. PMID 32058716 DOI: 10.1021/jacs.0c00269   
2020 Hyjek-Składanowska M, Vickers T, Napiórkowska A, Anderson B, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M. Origins of the increased affinity of phosphorothioate-modified therapeutic nucleic acids for proteins. Journal of the American Chemical Society. PMID 32202774 DOI: 10.1021/jacs.9b13524   
2020 Kim H, Kim JG, Muniyappan S, Kim TW, Lee SJ, Ihee H. Effect of Occluded Ligand Migration on the Kinetics and Structural Dynamics of Homodimeric Hemoglobin. The Journal of Physical Chemistry. B. PMID 32027135 DOI: 10.1021/acs.jpcb.9b11749   
2020 Riccardi C, Musumeci D, Platella C, Gaglione R, Arciello A, Montesarchio D. Tuning the Polymorphism of the Anti-VEGF G-rich V7t1 Aptamer by Covalent Dimeric Constructs. International Journal of Molecular Sciences. 21. PMID 32183039 DOI: 10.3390/ijms21061963   
2020 Tang H, Huang L, Sun C, Zhao D. Exploring the structure-activity relationship and interaction mechanism of flavonoids and α-glucosidase based on experimental analysis and molecular docking studies. Food & Function. PMID 32226990 DOI: 10.1039/c9fo02806d   
2020 Ochiai A, Ogawa K, Fukuda M, Suzuki M, Ito K, Tanaka T, Sagehashi Y, Taniguchi M. Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding. Journal of Bioscience and Bioengineering. PMID 32192842 DOI: 10.1016/j.jbiosc.2020.02.011   
2020 Sasmal S, Gill SC, Lim NM, Mobley DL. Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 32058713 DOI: 10.1021/acs.jctc.9b01066   
2020 Jeong KS, Seo SB, Lee S, Jeon HG. Dramatic Enhancement of Binding Affinities between Foldamer-Based Receptors and Anions by Intra-Receptor π-Stacking. Angewandte Chemie (International Ed. in English). PMID 32157775 DOI: 10.1002/anie.202002657   
2020 Glöckner S, Ngo K, Wagner B, Heine A, Klebe G. The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II. Biomolecules. 10. PMID 32230853 DOI: 10.3390/biom10040509   
2020 Agarwal S, Dixit A, Kashaw SK. Ligand and structure based virtual screening of chemical databases to explore potent small molecule inhibitors against breast invasive carcinoma using recent computational technologies. Journal of Molecular Graphics & Modelling. 98: 107591. PMID 32234678 DOI: 10.1016/j.jmgm.2020.107591   
2020 Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational changes in alkyl chains determine the thermodynamic and kinetic binding profiles of Carbonic Anhydrase inhibitors. Acs Chemical Biology. PMID 32027480 DOI: 10.1021/acschembio.9b00895   
2020 Jain M, Muthukumaran J, Singh AK. Structural and Functional characterization of Chitin binding Lectin from : Insights from Phylogenetic analysis, Protein structure prediction, Molecular docking and Molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics. 1-33. PMID 32116131 DOI: 10.1080/07391102.2020.1737234   
2020 Newberry RW, Leong JT, Chow ED, Kampmann M, DeGrado WF. Deep mutational scanning reveals the structural basis for α-synuclein activity. Nature Chemical Biology. PMID 32152544 DOI: 10.1038/s41589-020-0480-6   
2020 Myrhammar A, Rosik D, Eriksson Karlström A. Photo-controlled reversible binding between the protein A-derived Z domain and immunoglobulin G. Bioconjugate Chemistry. PMID 32027501 DOI: 10.1021/acs.bioconjchem.9b00786   
2020 Zhong S, Huang K, Luo S, Dong S, Duan L. Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method. Physical Chemistry Chemical Physics : Pccp. PMID 32043094 DOI: 10.1039/c9cp06459a   
2020 Salifu EY, Agoni C, Olotu FA, Soliman MES. Triple Mycobacterial ATP-synthase mutations impedes Bedaquiline binding: Atomistic and structural perspectives. Computational Biology and Chemistry. 85: 107204. PMID 31981966 DOI: 10.1016/j.compbiolchem.2020.107204   
2020 Omahdi Z, Horikawa Y, Nagae M, Toyonaga K, Imamura A, Takato K, Teramoto T, Ishida H, Kakuta Y, Yamasaki S. Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR. The Journal of Biological Chemistry. PMID 32139512 DOI: 10.1074/jbc.RA120.012491   
2020 De Oliveira TV, Guimarães AP, Bressan GC, Maia ER, Coimbra JSDR, Polêto MD, De Oliveira EB. Structural and Molecular Bases of Angiotensin-Converting Enzyme Inhibition by Bovine Casein-Derived Peptides: An Molecular Dynamics Approach. Journal of Biomolecular Structure & Dynamics. 1-29. PMID 32066337 DOI: 10.1080/07391102.2020.1730243   
2020 Heifetz A, Morao I, Babu MM, James T, Southey MW, Fedorov DG, Aldeghi M, Bodkin MJ, Townsend-Nicholson A. Characterising Inter-helical Interactions of G Protein-Coupled Receptors with the Fragment Molecular Orbital Method. Journal of Chemical Theory and Computation. PMID 32096994 DOI: 10.1021/acs.jctc.9b01136   
2020 Ullah R, Shehzad A, Shah MA, March M, Ismat F, Iqbal M, Onesti S, Rahman M, McPherson MJ. C-Terminal Domain of the Human Zinc Transporter hZnT8 Is Structurally Indistinguishable from Its Disease Risk Variant (R325W). International Journal of Molecular Sciences. 21. PMID 32023808 DOI: 10.3390/ijms21030926   
2020 Huang S, Li H, Liu Y, Yang L, Wang D, Xiao Q. Investigations of conformational structure and enzymatic activity of trypsin after its binding interaction with graphene oxide. Journal of Hazardous Materials. 392: 122285. PMID 32105952 DOI: 10.1016/j.jhazmat.2020.122285   
2020 Allert MJ, Hellinga HW. Describing complex structure-function relationships in biomolecules at equilibrium. Journal of Molecular Biology. PMID 31940471 DOI: 10.1016/j.jmb.2019.12.039   
2020 O'Brien KT, Mooney C, Lopez C, Pollastri G, Shields DC. Prediction of polyproline II secondary structure propensity in proteins. Royal Society Open Science. 7: 191239. PMID 32218953 DOI: 10.1098/rsos.191239   
2020 Wang C, Shi D, Zhang F, Yu X, Lin G, Zhou Z. Characterization of binding interaction between magnesium isoglycyrrhizinate and human serum albumin. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 234: 118245. PMID 32179463 DOI: 10.1016/j.saa.2020.118245