Статті в журналах з теми "Quality assessment of protein-ligand crystal structures"
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Chakraborti, Sohini, Kaushik Hatti, and 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, no. 13 (June 25, 2021): 6830. http://dx.doi.org/10.3390/ijms22136830.
Повний текст джерелаJaskolski, Mariusz, Zbigniew Dauter, Ivan G. Shabalin, Miroslaw Gilski, Dariusz Brzezinski, Marcin Kowiel, Bernhard Rupp, and Alexander Wlodawer. "Crystallographic models of SARS-CoV-2 3CLpro: in-depth assessment of structure quality and validation." IUCrJ 8, no. 2 (February 9, 2021): 238–56. http://dx.doi.org/10.1107/s2052252521001159.
Повний текст джерелаShelley, Kathryn L., Thomas P. E. Dixon, Jonathan C. Brooks-Bartlett, and Elspeth F. Garman. "RABDAM: quantifying specific radiation damage in individual protein crystal structures." Journal of Applied Crystallography 51, no. 2 (March 28, 2018): 552–59. http://dx.doi.org/10.1107/s1600576718002509.
Повний текст джерелаDas, Debanu, Matthew Duncton, Patricia Pellicena, Ashley Deacon, David Wilson, and Millie Georgiadis. "Development of a DNA damage response (DDR) therapeutics platform for oncology." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): e15036-e15036. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.e15036.
Повний текст джерелаRambo, Robert, Greg Hura, Michal Hammel, and John Tainer. "X-ray scattering methods for accurate analyses of flexible complexes." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C409. http://dx.doi.org/10.1107/s2053273314095904.
Повний текст джерелаHassan, Heba H. A., Muhammad I. Ismail, Mohammed A. S. Abourehab, Frank M. Boeckler, Tamer M. Ibrahim, and Reem K. Arafa. "In Silico Targeting of Fascin Protein for Cancer Therapy: Benchmarking, Virtual Screening and Molecular Dynamics Approaches." Molecules 28, no. 3 (January 29, 2023): 1296. http://dx.doi.org/10.3390/molecules28031296.
Повний текст джерелаHaghighi, Fatemeh, Semen Yesylevskyy, Siamak Davani, and Christophe Ramseyer. "Membrane Environment Modulates Ligand-Binding Propensity of P2Y12 Receptor." Pharmaceutics 13, no. 4 (April 9, 2021): 524. http://dx.doi.org/10.3390/pharmaceutics13040524.
Повний текст джерелаMoreno-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, no. 6 (October 10, 2019): 1074–85. http://dx.doi.org/10.1107/s2052252519011655.
Повний текст джерелаRidhwan, Mohamad Jemain Mohamad, Syahrul Imran Abu Bakar, Normala Abd Latip, Nurunajah Ab Ghani, and 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, no. 03 (February 17, 2022): 259–85. http://dx.doi.org/10.1142/s2737416522300012.
Повний текст джерелаWang, Meng-yu, Peng Li, and 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.
Повний текст джерелаMartin, J. L. "Protein Crystallography and Examples of its Applications in Medicinal Chemistry." Current Medicinal Chemistry 3, no. 6 (December 1999): 419–36. http://dx.doi.org/10.2174/0929867303666220307175609.
Повний текст джерелаIershov, Anton, Konstantin Odynets, Alexander Kornelyuk, and Vadim Kavsan. "Homology modeling of 3D structure of human chitinase-like protein CHI3L2." Open Life Sciences 5, no. 4 (August 1, 2010): 407–20. http://dx.doi.org/10.2478/s11535-010-0039-8.
Повний текст джерелаRai, Brajesh K., Vishnu Sresht, Qingyi Yang, Ray Unwalla, Meihua Tu, Alan M. Mathiowetz, and 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, no. 10 (October 2019): 4195–208. http://dx.doi.org/10.1021/acs.jcim.9b00373.
Повний текст джерелаSadybekov, 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, no. 12 (December 3, 2020): 1634. http://dx.doi.org/10.3390/biom10121634.
Повний текст джерелаKapla, Jon, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent, and Jens Carlsson. "Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?" PLOS Computational Biology 17, no. 5 (May 13, 2021): e1008936. http://dx.doi.org/10.1371/journal.pcbi.1008936.
Повний текст джерелаLieske, 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, no. 4 (June 19, 2019): 714–28. http://dx.doi.org/10.1107/s2052252519007395.
Повний текст джерелаVidad, Ashley Ryan, Stephen Macaspac, and Ho Leung Ng. "Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation." PeerJ 9 (September 24, 2021): e12219. http://dx.doi.org/10.7717/peerj.12219.
Повний текст джерелаAlex, Jimi M., Martin L. Rennie, Sylvain Engilberge, Gábor Lehoczki, Hajdu Dorottya, Ádám Fizil, Gyula Batta, and Peter B. Crowley. "Calixarene-mediated assembly of a small antifungal protein." IUCrJ 6, no. 2 (February 5, 2019): 238–47. http://dx.doi.org/10.1107/s2052252519000411.
Повний текст джерелаZhao, Haifan, Heng Zhang, Zhun She, Zengqiang Gao, Qi Wang, Zhi Geng, and 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, no. 3 (February 1, 2023): 2740. http://dx.doi.org/10.3390/ijms24032740.
Повний текст джерелаLokwani, Deepak K., Aniket P. Sarkate, Kshipra S. Karnik, Anna Pratima G. Nikalje, and 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, no. 7 (April 1, 2020): 1622. http://dx.doi.org/10.3390/molecules25071622.
Повний текст джерелаJanowski, Pawel A., Nigel W. Moriarty, Brian P. Kelley, David A. Case, Darrin M. York, Paul D. Adams, and Gregory L. Warren. "Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX." Acta Crystallographica Section D Structural Biology 72, no. 9 (August 31, 2016): 1062–72. http://dx.doi.org/10.1107/s2059798316012225.
Повний текст джерелаNakatani, Yoshio, Wanting Jiao, David Aragão, Yosuke Shimaki, Jessica Petri, Emily J. Parker, and 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, no. 10 (September 23, 2017): 541–49. http://dx.doi.org/10.1107/s2053230x17013073.
Повний текст джерелаChopra, Deepak, and Dhananjay Dey. "Computational approaches towards crystal engineering in molecular crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C642. http://dx.doi.org/10.1107/s2053273314093577.
Повний текст джерелаLim, Victoria T., David F. Hahn, Gary Tresadern, Christopher I. Bayly, and David L. Mobley. "Benchmark assessment of molecular geometries and energies from small molecule force fields." F1000Research 9 (December 3, 2020): 1390. http://dx.doi.org/10.12688/f1000research.27141.1.
Повний текст джерелаGoldsmith, Michael-Rock, Christopher M. Grulke, Daniel T. Chang, Thomas R. Transue, Stephen B. Little, James R. Rabinowitz, and Rogelio Tornero-Velez. "DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology." Dataset Papers in Science 2014 (November 11, 2014): 1–5. http://dx.doi.org/10.1155/2014/421693.
Повний текст джерелаWallace, B. A. "Protein characterisation by synchrotron radiation circular dichroism spectroscopy." Quarterly Reviews of Biophysics 42, no. 4 (November 2009): 317–70. http://dx.doi.org/10.1017/s003358351000003x.
Повний текст джерелаZeng, Zhen-Fang, Qiu-Ping Huang, Jie-Hui Cai, Guang-Jin Zheng, Qiu-Chan Huang, Zi-Lu Liu, Zi-Lu Chen, and 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, no. 13 (July 1, 2021): 4028. http://dx.doi.org/10.3390/molecules26134028.
Повний текст джерелаDu, Hongyan, Junbo Gao, Gaoqi Weng, Junjie Ding, Xin Chai, Jinping Pang, Yu Kang, Dan Li, Dongsheng Cao, and Tingjun Hou. "CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors." Nucleic Acids Research 49, no. D1 (October 17, 2020): D1122—D1129. http://dx.doi.org/10.1093/nar/gkaa876.
Повний текст джерелаMandal, Suraj Kumar, and 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, no. 12 (November 11, 2021): 1516–34. http://dx.doi.org/10.1107/s2059798321010457.
Повний текст джерелаOo, Adrian, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly Abu Bakar, and Keivan Zandi. "In silico study on anti-Chikungunya virus activity of hesperetin." PeerJ 4 (October 26, 2016): e2602. http://dx.doi.org/10.7717/peerj.2602.
Повний текст джерелаDelfosse, Vanessa, Marina Grimaldi, Jean-Luc Pons, Vincent Cavaillès, Gilles Labesse, Patrick Balaguer, and William Bourguet. "Structural and functional profiling of estrogen receptors environmental ligands." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1399. http://dx.doi.org/10.1107/s2053273314086008.
Повний текст джерелаRana, Rabia Mukhtar, Shailima Rampogu, Noman Bin Abid, Amir Zeb, Shraddha Parate, Gihwan Lee, Sanghwa Yoon, Yumi Kim, Donghwan Kim, and Keun Woo Lee. "In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics." Molecules 25, no. 15 (July 31, 2020): 3510. http://dx.doi.org/10.3390/molecules25153510.
Повний текст джерелаMiyaguchi, Ikuko, Miwa Sato, Akiko Kashima, Hiroyuki Nakagawa, Yuichi Kokabu, Biao Ma, Shigeyuki Matsumoto, Atsushi Tokuhisa, Masateru Ohta, and Mitsunori Ikeguchi. "Machine learning to estimate the local quality of protein crystal structures." Scientific Reports 11, no. 1 (December 2021). http://dx.doi.org/10.1038/s41598-021-02948-y.
Повний текст джерелаClark, Jordan J., Zachary J. Orban, and Heather A. Carlson. "Predicting binding sites from unbound versus bound protein structures." Scientific Reports 10, no. 1 (September 28, 2020). http://dx.doi.org/10.1038/s41598-020-72906-7.
Повний текст джерелаAlzyoud, Lara, Richard A. Bryce, Mohammad Al Sorkhy, Noor Atatreh, and Mohammad A. Ghattas. "Structure-based assessment and druggability classification of protein–protein interaction sites." Scientific Reports 12, no. 1 (May 13, 2022). http://dx.doi.org/10.1038/s41598-022-12105-8.
Повний текст джерелаVeit-Acosta, Martina, and 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 (February 10, 2021). http://dx.doi.org/10.2174/0929867328666210210121320.
Повний текст джерелаHenkel, Alessandra, Marina Galchenkova, Julia Maracke, Oleksandr Yefanov, Bjarne Klopprogge, Johanna Hakanpää, Jeroen R. Mesters, Henry N. Chapman, and Dominik Oberthuer. "JINXED: just in time crystallization for easy structure determination of biological macromolecules." IUCrJ 10, no. 3 (March 9, 2023). http://dx.doi.org/10.1107/s2052252523001653.
Повний текст джерелаGarcía-Nafría, Javier, Yang Lee, Xiaochen Bai, Byron Carpenter, and Christopher G. Tate. "Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein." eLife 7 (May 4, 2018). http://dx.doi.org/10.7554/elife.35946.
Повний текст джерелаMeller, Artur, Saulo De Oliveira, Aram Davtyan, Tigran Abramyan, Gregory R. Bowman, and 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 (April 18, 2023). http://dx.doi.org/10.3389/fmolb.2023.1171143.
Повний текст джерелаStachowski, Timothy R., and Marcus Fischer. "FLEXR: automated multi-conformer model building using electron-density map sampling." Acta Crystallographica Section D Structural Biology 79, no. 5 (April 18, 2023). http://dx.doi.org/10.1107/s2059798323002498.
Повний текст джерелаSacco, Michael D., Kyle G. Kroeck, M. Trent Kemp, Xiujun Zhang, Logan D. Andrews та 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, № 1 (4 листопада 2019). http://dx.doi.org/10.1128/aac.01473-19.
Повний текст джерелаAWofisayo, Oladoja. "IN SILICO ANTIMALARIAL TARGET SELECTION CONSERVED IN FOUR PLASMODIUM SPECIES." Universal Journal of Pharmaceutical Research, November 15, 2020. http://dx.doi.org/10.22270/ujpr.v5i5.483.
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