Artículos de revistas sobre el tema "Quality assessment of protein-ligand crystal structures"
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Chakraborti, Sohini, Kaushik Hatti y Narayanaswamy Srinivasan. "‘All That Glitters Is Not Gold’: High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses". International Journal of Molecular Sciences 22, n.º 13 (25 de junio de 2021): 6830. http://dx.doi.org/10.3390/ijms22136830.
Texto completoJaskolski, Mariusz, Zbigniew Dauter, Ivan G. Shabalin, Miroslaw Gilski, Dariusz Brzezinski, Marcin Kowiel, Bernhard Rupp y Alexander Wlodawer. "Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation". IUCrJ 8, n.º 2 (9 de febrero de 2021): 238–56. http://dx.doi.org/10.1107/s2052252521001159.
Texto completoShelley, Kathryn L., Thomas P. E. Dixon, Jonathan C. Brooks-Bartlett y Elspeth F. Garman. "RABDAM: quantifying specific radiation damage in individual protein crystal structures". Journal of Applied Crystallography 51, n.º 2 (28 de marzo de 2018): 552–59. http://dx.doi.org/10.1107/s1600576718002509.
Texto completoDas, Debanu, Matthew Duncton, Patricia Pellicena, Ashley Deacon, David Wilson y Millie Georgiadis. "Development of a DNA damage response (DDR) therapeutics platform for oncology." Journal of Clinical Oncology 39, n.º 15_suppl (20 de mayo de 2021): e15036-e15036. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15036.
Texto completoRambo, Robert, Greg Hura, Michal Hammel y John Tainer. "X-ray scattering methods for accurate analyses of flexible complexes". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 de agosto de 2014): C409. http://dx.doi.org/10.1107/s2053273314095904.
Texto completoHassan, Heba H. A., Muhammad I. Ismail, Mohammed A. S. Abourehab, Frank M. Boeckler, Tamer M. Ibrahim y Reem K. Arafa. "In Silico Targeting of Fascin Protein for Cancer Therapy: Benchmarking, Virtual Screening and Molecular Dynamics Approaches". Molecules 28, n.º 3 (29 de enero de 2023): 1296. http://dx.doi.org/10.3390/molecules28031296.
Texto completoHaghighi, Fatemeh, Semen Yesylevskyy, Siamak Davani y Christophe Ramseyer. "Membrane Environment Modulates Ligand-Binding Propensity of P2Y12 Receptor". Pharmaceutics 13, n.º 4 (9 de abril de 2021): 524. http://dx.doi.org/10.3390/pharmaceutics13040524.
Texto completoMoreno-Chicano, Tadeo, Ali Ebrahim, Danny Axford, Martin V. Appleby, John H. Beale, Amanda K. Chaplin, Helen M. E. Duyvesteyn et al. "High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography". IUCrJ 6, n.º 6 (10 de octubre de 2019): 1074–85. http://dx.doi.org/10.1107/s2052252519011655.
Texto completoRidhwan, Mohamad Jemain Mohamad, Syahrul Imran Abu Bakar, Normala Abd Latip, Nurunajah Ab Ghani y Nor Hadiani Ismail. "A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies". Journal of Computational Biophysics and Chemistry 21, n.º 03 (17 de febrero de 2022): 259–85. http://dx.doi.org/10.1142/s2737416522300012.
Texto completoWang, Meng-yu, Peng Li y Pei-li Qiao. "The Virtual Screening of the Drug Protein with a Few Crystal Structures Based on the Adaboost-SVM". Computational and Mathematical Methods in Medicine 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/4809831.
Texto completoMartin, J. L. "Protein Crystallography and Examples of its Applications in Medicinal Chemistry". Current Medicinal Chemistry 3, n.º 6 (diciembre de 1999): 419–36. http://dx.doi.org/10.2174/0929867303666220307175609.
Texto completoIershov, Anton, Konstantin Odynets, Alexander Kornelyuk y Vadim Kavsan. "Homology modeling of 3D structure of human chitinase-like protein CHI3L2". Open Life Sciences 5, n.º 4 (1 de agosto de 2010): 407–20. http://dx.doi.org/10.2478/s11535-010-0039-8.
Texto completoRai, Brajesh K., Vishnu Sresht, Qingyi Yang, Ray Unwalla, Meihua Tu, Alan M. Mathiowetz y Gregory A. Bakken. "Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations". Journal of Chemical Information and Modeling 59, n.º 10 (octubre de 2019): 4195–208. http://dx.doi.org/10.1021/acs.jcim.9b00373.
Texto completoSadybekov, Arman A., Rebecca L. Brouillette, Egor Marin, Anastasiia V. Sadybekov, Aleksandra Luginina, Anastasiia Gusach, Alexey Mishin et al. "Structure-Based Virtual Screening of Ultra-Large Library Yields Potent Antagonists for a Lipid GPCR". Biomolecules 10, n.º 12 (3 de diciembre de 2020): 1634. http://dx.doi.org/10.3390/biom10121634.
Texto completoKapla, Jon, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent y Jens Carlsson. "Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?" PLOS Computational Biology 17, n.º 5 (13 de mayo de 2021): e1008936. http://dx.doi.org/10.1371/journal.pcbi.1008936.
Texto completoLieske, Julia, Maximilian Cerv, Stefan Kreida, Dana Komadina, Janine Fischer, Miriam Barthelmess, Pontus Fischer et al. "On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies". IUCrJ 6, n.º 4 (19 de junio de 2019): 714–28. http://dx.doi.org/10.1107/s2052252519007395.
Texto completoVidad, Ashley Ryan, Stephen Macaspac y Ho Leung Ng. "Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation". PeerJ 9 (24 de septiembre de 2021): e12219. http://dx.doi.org/10.7717/peerj.12219.
Texto completoAlex, Jimi M., Martin L. Rennie, Sylvain Engilberge, Gábor Lehoczki, Hajdu Dorottya, Ádám Fizil, Gyula Batta y Peter B. Crowley. "Calixarene-mediated assembly of a small antifungal protein". IUCrJ 6, n.º 2 (5 de febrero de 2019): 238–47. http://dx.doi.org/10.1107/s2052252519000411.
Texto completoZhao, Haifan, Heng Zhang, Zhun She, Zengqiang Gao, Qi Wang, Zhi Geng y Yuhui Dong. "Exploring AlphaFold2′s Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein". International Journal of Molecular Sciences 24, n.º 3 (1 de febrero de 2023): 2740. http://dx.doi.org/10.3390/ijms24032740.
Texto completoLokwani, Deepak K., Aniket P. Sarkate, Kshipra S. Karnik, Anna Pratima G. Nikalje y Julio A. Seijas. "Structure-Based Site of Metabolism (SOM) Prediction of Ligand for CYP3A4 Enzyme: Comparison of Glide XP and Induced Fit Docking (IFD)". Molecules 25, n.º 7 (1 de abril de 2020): 1622. http://dx.doi.org/10.3390/molecules25071622.
Texto completoJanowski, Pawel A., Nigel W. Moriarty, Brian P. Kelley, David A. Case, Darrin M. York, Paul D. Adams y Gregory L. Warren. "Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX". Acta Crystallographica Section D Structural Biology 72, n.º 9 (31 de agosto de 2016): 1062–72. http://dx.doi.org/10.1107/s2059798316012225.
Texto completoNakatani, Yoshio, Wanting Jiao, David Aragão, Yosuke Shimaki, Jessica Petri, Emily J. Parker y Gregory M. Cook. "Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å". Acta Crystallographica Section F Structural Biology Communications 73, n.º 10 (23 de septiembre de 2017): 541–49. http://dx.doi.org/10.1107/s2053230x17013073.
Texto completoChopra, Deepak y Dhananjay Dey. "Computational approaches towards crystal engineering in molecular crystals". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 de agosto de 2014): C642. http://dx.doi.org/10.1107/s2053273314093577.
Texto completoLim, Victoria T., David F. Hahn, Gary Tresadern, Christopher I. Bayly y David L. Mobley. "Benchmark assessment of molecular geometries and energies from small molecule force fields". F1000Research 9 (3 de diciembre de 2020): 1390. http://dx.doi.org/10.12688/f1000research.27141.1.
Texto completoGoldsmith, Michael-Rock, Christopher M. Grulke, Daniel T. Chang, Thomas R. Transue, Stephen B. Little, James R. Rabinowitz y Rogelio Tornero-Velez. "DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology". Dataset Papers in Science 2014 (11 de noviembre de 2014): 1–5. http://dx.doi.org/10.1155/2014/421693.
Texto completoWallace, B. A. "Protein characterisation by synchrotron radiation circular dichroism spectroscopy". Quarterly Reviews of Biophysics 42, n.º 4 (noviembre de 2009): 317–70. http://dx.doi.org/10.1017/s003358351000003x.
Texto completoZeng, Zhen-Fang, Qiu-Ping Huang, Jie-Hui Cai, Guang-Jin Zheng, Qiu-Chan Huang, Zi-Lu Liu, Zi-Lu Chen y You-Huan Wei. "Synthesis, Characterization, DNA/HSA Interactions, and Anticancer Activity of Two Novel Copper(II) Complexes with 4-Chloro-3-Nitrobenzoic Acid Ligand". Molecules 26, n.º 13 (1 de julio de 2021): 4028. http://dx.doi.org/10.3390/molecules26134028.
Texto completoDu, Hongyan, Junbo Gao, Gaoqi Weng, Junjie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dongsheng Cao y Tingjun Hou. "CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors". Nucleic Acids Research 49, n.º D1 (17 de octubre de 2020): D1122—D1129. http://dx.doi.org/10.1093/nar/gkaa876.
Texto completoMandal, Suraj Kumar y Shankar Prasad Kanaujia. "Structural and thermodynamic insights into a novel Mg2+–citrate-binding protein from the ABC transporter superfamily". Acta Crystallographica Section D Structural Biology 77, n.º 12 (11 de noviembre de 2021): 1516–34. http://dx.doi.org/10.1107/s2059798321010457.
Texto completoOo, Adrian, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly Abu Bakar y Keivan Zandi. "In silico study on anti-Chikungunya virus activity of hesperetin". PeerJ 4 (26 de octubre de 2016): e2602. http://dx.doi.org/10.7717/peerj.2602.
Texto completoDelfosse, Vanessa, Marina Grimaldi, Jean-Luc Pons, Vincent Cavaillès, Gilles Labesse, Patrick Balaguer y William Bourguet. "Structural and functional profiling of estrogen receptors environmental ligands". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 de agosto de 2014): C1399. http://dx.doi.org/10.1107/s2053273314086008.
Texto completoRana, Rabia Mukhtar, Shailima Rampogu, Noman Bin Abid, Amir Zeb, Shraddha Parate, Gihwan Lee, Sanghwa Yoon, Yumi Kim, Donghwan Kim y Keun Woo Lee. "In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics". Molecules 25, n.º 15 (31 de julio de 2020): 3510. http://dx.doi.org/10.3390/molecules25153510.
Texto completoMiyaguchi, Ikuko, Miwa Sato, Akiko Kashima, Hiroyuki Nakagawa, Yuichi Kokabu, Biao Ma, Shigeyuki Matsumoto, Atsushi Tokuhisa, Masateru Ohta y Mitsunori Ikeguchi. "Machine learning to estimate the local quality of protein crystal structures". Scientific Reports 11, n.º 1 (diciembre de 2021). http://dx.doi.org/10.1038/s41598-021-02948-y.
Texto completoClark, Jordan J., Zachary J. Orban y Heather A. Carlson. "Predicting binding sites from unbound versus bound protein structures". Scientific Reports 10, n.º 1 (28 de septiembre de 2020). http://dx.doi.org/10.1038/s41598-020-72906-7.
Texto completoAlzyoud, Lara, Richard A. Bryce, Mohammad Al Sorkhy, Noor Atatreh y Mohammad A. Ghattas. "Structure-based assessment and druggability classification of protein–protein interaction sites". Scientific Reports 12, n.º 1 (13 de mayo de 2022). http://dx.doi.org/10.1038/s41598-022-12105-8.
Texto completoVeit-Acosta, Martina y Walter Filgueira de Azevedo Junior. "The Impact of CrystallographicData for the Development of Machine Learning Models to Predict Protein-Ligand Binding Affinity". Current Medicinal Chemistry 28 (10 de febrero de 2021). http://dx.doi.org/10.2174/0929867328666210210121320.
Texto completoHenkel, Alessandra, Marina Galchenkova, Julia Maracke, Oleksandr Yefanov, Bjarne Klopprogge, Johanna Hakanpää, Jeroen R. Mesters, Henry N. Chapman y Dominik Oberthuer. "JINXED: just in time crystallization for easy structure determination of biological macromolecules". IUCrJ 10, n.º 3 (9 de marzo de 2023). http://dx.doi.org/10.1107/s2052252523001653.
Texto completoGarcía-Nafría, Javier, Yang Lee, Xiaochen Bai, Byron Carpenter y Christopher G. Tate. "Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein". eLife 7 (4 de mayo de 2018). http://dx.doi.org/10.7554/elife.35946.
Texto completoMeller, Artur, Saulo De Oliveira, Aram Davtyan, Tigran Abramyan, Gregory R. Bowman y Henry van den Bedem. "Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors". Frontiers in Molecular Biosciences 10 (18 de abril de 2023). http://dx.doi.org/10.3389/fmolb.2023.1171143.
Texto completoStachowski, Timothy R. y Marcus Fischer. "FLEXR: automated multi-conformer model building using electron-density map sampling". Acta Crystallographica Section D Structural Biology 79, n.º 5 (18 de abril de 2023). http://dx.doi.org/10.1107/s2059798323002498.
Texto completoSacco, Michael D., Kyle G. Kroeck, M. Trent Kemp, Xiujun Zhang, Logan D. Andrews y Yu Chen. "Influence of the α-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 β-Lactamase". Antimicrobial Agents and Chemotherapy 64, n.º 1 (4 de noviembre de 2019). http://dx.doi.org/10.1128/aac.01473-19.
Texto completoAWofisayo, Oladoja. "IN SILICO ANTIMALARIAL TARGET SELECTION CONSERVED IN FOUR PLASMODIUM SPECIES". Universal Journal of Pharmaceutical Research, 15 de noviembre de 2020. http://dx.doi.org/10.22270/ujpr.v5i5.483.
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