Philip Biggin - Related publications

2011- Biochemistry University of Oxford, Oxford, United Kingdom 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Camacho-Hernandez GA, Taylor P. Lessons from nature: Structural studies and drug design driven by a homologous surrogate from invertebrates, AChBP. Neuropharmacology. 108108. PMID 32353365 DOI: 10.1016/j.neuropharm.2020.108108   
2020 Kumar SP, Patel CN, Rawal RM, Pandya HA. Energetic contributions of amino acid residues and its cross-talk (ECONTACT) to delineate ligand binding mechanism. Proteins. PMID 32323374 DOI: 10.1002/prot.25894   
2020 Brodzki M, Michałowski MA, Gos M, Mozrzymas JW. Mutations of αF45 residue of GABA receptor loop G reveal its involvement in agonist binding and channel opening/closing transitions. Biochemical Pharmacology. 177: 113917. PMID 32194055 DOI: 10.1016/j.bcp.2020.113917   
2020 Thapa B, Erickson J, Raghavachari K. Quantum Mechanical Investigation of Three-Dimensional Activity Cliffs Using the Molecules-in-Molecules Fragmentation-Based Method. Journal of Chemical Information and Modeling. PMID 32407081 DOI: 10.1021/acs.jcim.9b01123   
2020 Feng J, Shukla D. FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution. The Journal of Physical Chemistry. B. PMID 32283936 DOI: 10.1021/acs.jpcb.9b11869   
2020 Wu FJ, Williams LM, Abdul-Ridha A, Gunatilaka A, Vaid TM, Kocan M, Whitehead AR, Griffin MDW, Bathgate RAD, Scott DJ, Gooley PR. Probing the correlation between ligand efficacy and conformational diversity at the α1A-adrenoreceptor reveals allosteric coupling of its microswitches. The Journal of Biological Chemistry. PMID 32303636 DOI: 10.1074/jbc.RA120.012842   
2020 Nakliang P, Lazim R, Chang H, Choi S. Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies. Biomolecules. 10. PMID 32325877 DOI: 10.3390/biom10040631   
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 Chu WT, Shammas SL, Wang J. Charge Interactions Modulate the Encounter Complex Ensemble of Two Differently Charged Disordered Protein Partners of KIX. Journal of Chemical Theory and Computation. PMID 32325001 DOI: 10.1021/acs.jctc.9b01264   
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 Wahedi HM, Ahmad S, Abbasi SW. Stilbene-based Natural Compounds as Promising Drug Candidates against COVID-19. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32345140 DOI: 10.1080/07391102.2020.1762743   
2020 Harris D, Muzzopappa F, Glaser F, Wilson A, Kirilovsky D, Adir N. Structural dynamics in the C terminal domain homolog of orange carotenoid protein reveals residues critical for carotenoid uptake. Biochimica Et Biophysica Acta. Bioenergetics. 148214. PMID 32360310 DOI: 10.1016/j.bbabio.2020.148214   
2020 Guest EE, Oatley SA, Macdonald SJF, Hirst JD. Molecular Simulation of αVβ6 Integrin Inhibitors. Journal of Chemical Information and Modeling. PMID 32421320 DOI: 10.1021/acs.jcim.0c00254   
2020 Chen Q, Wang F, Zhou B. Investigations of Retinoic Acid Receptor-Related Orphan Receptor-Ramma t (RORγt) Agonists: A Combination of 3D-QSAR, Molecular Docking and Molecular Dynamics. Journal of Biomolecular Structure & Dynamics. 1-19. PMID 32375589 DOI: 10.1080/07391102.2020.1765873   
2020 Qiao P, Liu Y, Zhang T, Benavides A, Laganowsky A. Insight into the selectivity of Kir3.2 toward phosphatidylinositides. Biochemistry. PMID 32372643 DOI: 10.1021/acs.biochem.0c00163   
2020 Robustelli P, Piana S, Shaw DE. The mechanism of coupled folding-upon-binding of an intrinsically disordered protein. Journal of the American Chemical Society. PMID 32323533 DOI: 10.1021/jacs.0c03217   
2020 Larsen AH, Wang Y, Bottaro S, Grudinin S, Arleth L, Lindorff-Larsen K. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution. Plos Computational Biology. 16: e1007870. PMID 32339173 DOI: 10.1371/journal.pcbi.1007870   
2020 Bagchi A. Latest trends in structure based drug design with protein targets. Advances in Protein Chemistry and Structural Biology. 121: 1-23. PMID 32312418 DOI: 10.1016/bs.apcsb.2019.11.008   
2020 Smith JK, Pfaendtner J. Elucidating the Molecular Interactions Between Uremic Toxins and the Sudlow II Binding Site of Human Serum Albumin. The Journal of Physical Chemistry. B. PMID 32338898 DOI: 10.1021/acs.jpcb.0c02015   
2020 Moesgaard L, Reinholdt P, Wüstner D, Kongsted J. Modeling the sterol-binding domain of Aster-A provides insight into its multi-ligand specificity. Journal of Chemical Information and Modeling. PMID 32233488 DOI: 10.1021/acs.jcim.0c00086   
2020 Wang Q, Chen Y, Li S, Yang W, Sun L, Jang M, Wu X, Wang Q, Chen L, Wu Y. Ca-based allosteric switches and shape shifting in RGLG1 VWA domain. Computational and Structural Biotechnology Journal. 18: 821-833. PMID 32308929 DOI: 10.1016/j.csbj.2020.03.023   
2020 Lee KY, Cheon SH, Kim DG, Lee SJ, Lee BJ. A structural study of TatD from elucidates a putative DNA-binding mode of a Mg-dependent nuclease. Iucrj. 7: 509-521. PMID 32431834 DOI: 10.1107/S2052252520003917   
2020 Lin FY, Huang J, Pandey P, Rupakheti C, Li J, Roux B, MacKerell AD. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. Journal of Chemical Theory and Computation. PMID 32282198 DOI: 10.1021/acs.jctc.0c00057   
2020 Xie YC, Eriksson LA, Zhang RB. Molecular dynamics study of the recognition of ATP by nucleic acid aptamers. Nucleic Acids Research. PMID 32442296 DOI: 10.1093/nar/gkaa428   
2020 Zhang H, Saravanan KM, Lin J, Liao L, Ng JT, Zhou J, Wei Y. DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation. Peerj. 8: e8864. PMID 32292649 DOI: 10.7717/peerj.8864   
2020 Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Science Advances. 6: eaay7919. PMID 32284973 DOI: 10.1126/sciadv.aay7919   
2020 Yadav DK, Kumar S, Choi EH, Chaudhary S, Kim MH. Computational Modeling on Aquaporin-3 as Skin Cancer Target: A Virtual Screening Study. Frontiers in Chemistry. 8: 250. PMID 32351935 DOI: 10.3389/fchem.2020.00250   
2020 Behnam MAM, Klein CDP. Conformational selection in the flaviviral NS2B-NS3 protease. Biochimie. PMID 32335227 DOI: 10.1016/j.biochi.2020.04.014   
2020 Olson MA. Disorder-Order Transitions in Conformational Selection of a Peptide by Ebola Virus Nucleoprotein. Acs Omega. 5: 5691-5697. PMID 32226846 DOI: 10.1021/acsomega.9b03581   
2020 Sullivan HJ, Wang X, Nogle S, Liao S, Wu C. To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations. Ppar Research. 2020: 5314187. PMID 32308671 DOI: 10.1155/2020/5314187   
2020 Lake PT, Davidson RB, Klem H, Hocky GM, McCullagh M. Residue-Level Allostery Propagates Through the Effective Coarse-Grained Hessian. Journal of Chemical Theory and Computation. PMID 32251581 DOI: 10.1021/acs.jctc.9b01149   
2020 Guterres H, Im W. Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 32227880 DOI: 10.1021/acs.jcim.0c00057   
2020 Shi X, Chuo SW, Liou SH, Goodin DB. Double electron-electron resonance shows that substrate but not inhibitors cause disorder in the F/G loop of CYP119 in solution. Biochemistry. PMID 32338502 DOI: 10.1021/acs.biochem.0c00171   
2020 Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. Journal of Chemical Theory and Computation. PMID 32324997 DOI: 10.1021/acs.jctc.9b01261   
2020 Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. Journal of Chemical Theory and Computation. PMID 32324997 DOI: 10.1021/acs.jctc.9b01261   
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 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 Chavan TS, Cheng RC, Jiang T, Mathews II, Stein RA, Koehl A, Mchaourab HS, Tajkhorshid E, Maduke M. A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the Cl/H transport cycle. Elife. 9. PMID 32310757 DOI: 10.7554/eLife.53479   
2020 Zhang YN, Zhang XQ, Zhang XC, Xu JW, Li LL, Zhu XY, Wang JJ, Wei JY, Mang DZ, Zhang F, Yuan X, Wu X. Key amino acid residues influencing binding affinities of pheromone binding protein from Athetis lepigone to two sex pheromones. Journal of Agricultural and Food Chemistry. PMID 32392414 DOI: 10.1021/acs.jafc.0c01572   
2020 Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules. 10. PMID 32403216 DOI: 10.3390/biom10050743   
2020 Zhao Y, Cortes-Huerto R, Kremer K, Rudzinski JF. Investigating the Conformational Ensembles of Intrinsically-Disordered Proteins With a Simple Physics-Based Model. The Journal of Physical Chemistry. B. PMID 32345021 DOI: 10.1021/acs.jpcb.0c01949   
2020 Hosny A, Ashton M, Gong Y, McGarry K. The development of a predictive model to identify potential HIV-1 attachment inhibitors. Computers in Biology and Medicine. 120: 103743. PMID 32421648 DOI: 10.1016/j.compbiomed.2020.103743   
2020 Khan MF, Machuca MA, Rahman MM, Koç C, Norton RS, Smith BJ, Roujeinikova A. Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Chemoreceptor Tlp3. Biomolecules. 10. PMID 32403336 DOI: 10.3390/biom10050744   
2020 Niu C, Zhao Y, Bobst CE, Savinov SN, Kaltashov IA. Identification of protein recognition elements within heparin chains using enzymatic foot-printing in solution and on-line SEC/MS. Analytical Chemistry. PMID 32347711 DOI: 10.1021/acs.analchem.0c00115   
2020 Wolf NM, Lee H, Zagal D, Nam JW, Oh DC, Lee H, Suh JW, Pauli GF, Cho S, Abad-Zapatero C. Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions. Acta Crystallographica. Section D, Structural Biology. 76: 458-471. PMID 32355042 DOI: 10.1107/S2059798320004027   
2020 Kawahara K, Yoshida T, Maruno T, Oki H, Ohkubo T, Koide T, Kobayashi Y. Spatiotemporal regulation of PEDF signaling by type I collagen remodeling. Proceedings of the National Academy of Sciences of the United States of America. 117: 11450-11458. PMID 32385162 DOI: 10.1073/pnas.2004034117   
2020 Han Y, Král P. Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2. Acs Nano. PMID 32286790 DOI: 10.1021/acsnano.0c02857   
2020 Chen Y, Zheng Y, Fong P, Mao S, Wang Q. The application of the MM/GBSA method in the binding pose prediction of FGFR inhibitors. Physical Chemistry Chemical Physics : Pccp. PMID 32328599 DOI: 10.1039/d0cp00831a   
2020 Dwivedi VD, Arya A, Sharma T, Sharma S, Patil SA, Gupta VK. Computational investigation of phytomolecules as resuscitation-promoting factor B (RpfB) inhibitors for clinical suppression of Mycobacterium tuberculosis dormancy reactivation. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 83: 104356. PMID 32438079 DOI: 10.1016/j.meegid.2020.104356   
2020 Jensen MR, Yabukarski F, Communie G, Condamine E, Mas C, Volchkova V, Tarbouriech N, Bourhis JM, Volchkov V, Blackledge M, Jamin M. Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1. Biophysical Journal. PMID 32348724 DOI: 10.1016/j.bpj.2020.04.010