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1. Full Text Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation studyElectronic supplementary information (ESI) available: Table S1. MM/GBSA free energy calculation for the 26 complexes based on the 5 ns MD simulations, Fig. S1. The best binding poses of GSKex1 predicted by the Glide SP/XP docking compared with that of DNMT1/SFG (PDB entry: 3SWR). SFG is colored blue, and the best binding poses of GSKex1 predicted by the Glide XP and SP are colored red and green, respectively. The binding pose of GSKex1 on DNMT3A predicted by the Glide XP is colored magenta, Fig. S2. The RMSDs of the Cα atoms of the protein in the six studied complexes as a function of simulation time, Fig. S3. The RMSDs of the heavy atoms of the ligands in the six studied complexes as a function of simulation time, Fig. S4. Residue-based RMSFs relative to the initial structure during the 150 ns MD simulations, Fig. S5. Comparison of the representative structures of DNMT1/DC-05 and DNMT3A/GSKex1 with the lowest RMSDs relative to the averaged structures extracted from the 150 ns MD trajectories. DNMT1 is colored green, and DNMT3A is colored magenta. The carbon backbone of DC-05 is colored yellow, Fig. S6. Comparison of the representative structures of DNMT1/DC-05 and DNMT3A/GSKex1 with the lowest RMSDs relative to the averaged structures extracted from the 150 ns MD trajectories. DNMT1 is colored green, and DNMT3A is colored magenta. The carbon backbone of GSKex1 is colored yellow, Fig. S7. Convergence of the PMFs given by the US simulations for (A) DNMT1/SFG, (B) DNMT1/DC-05, (C) DNMT1/GSKex1, (D) DNMT3A/SFG, (E) DNMT3A/DC-05, and (F) DNMT3A/GSKex1. See DOI: 10.1039/c9cp02024a
ISSN 1463-9076, 6/2019, Volume 21, Issue 24, pp. 12931 - 12947
DNA methyltransferases (DNMTs), responsible for the regulation of DNA methylation, have been regarded as promising drug targets for cancer therapy. However,... 
Journal Article
2. Full Text Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study (Electronic supplementary information (ESI) available: Table S1. MM/GBSA free energy calculation for the 26 complexes based on the 5 ns MD simulations, Fig. S1. The best binding poses of GSKex1 predicted by the Glide SP/XP docking compared with that of DNMT1/SFG (PDB entry: 3SWR). SFG is colored blue, and the best binding poses of GSKex1 predicted by the Glide XP and SP are colored red and green, respectively. The binding pose of GSKex1 on DNMT3A predicted by the Glide XP is colored magenta, Fig. S2. The RMSDs of the Cα atoms of the protein in the six studied complexes as a function of simulation time, Fig. S3. The RMSDs of the heavy atoms of the ligands in the six studied complexes as a function of simulation time, Fig. S4. Residue-based RMSFs relative to the initial structure during the 150 ns MD simulations, Fig. S5. Comparison of the representative structures of DNMT1/DC-05 and DNMT3A/GSKex1 with the lowest RMSDs relative to the averaged structures extracted from the 150 ns MD trajectories. DNMT1 is colored green, and DNMT3A is colored magenta. The carbon backbone of DC-05 is colored yellow, Fig. S6. Comparison of the representative structures of DNMT1/DC-05 and DNMT3A/GSKex1 with the lowest RMSDs relative to the averaged structures extracted from the 150 ns MD trajectories. DNMT1 is colored green, and DNMT3A is colored magenta. The carbon backbone of GSKex1 is colored yellow, Fig. S7. Convergence of the PMFs given by the US simulations for (A) DNMT1/SFG, (B) DNMT1/DC-05, (C) DNMT1/GSKex1, (D) DNMT3A/SFG, (E) DNMT3A/DC-05, and (F) DNMT3A/GSKex1. See DOI: 10.1039/c9cp02024a)
Physical Chemistry Chemical Physics : PCCP, ISSN 1463-9076, 01/2019, Volume 21, Issue 24, pp. 12931 - 12947
DNA methyltransferases (DNMTs), responsible for the regulation of DNA methylation, have been regarded as promising drug targets for cancer therapy. However,... 
Binding | Backbone | Molecular dynamics | Trajectories | Selectivity | Carbon | Free energy | Proteins | Domains | Dynamic tests | Inhibitors | Simulation | Mathematical analysis | Selective binding | Predictions | DNA methylation | Docking | Catalysis | Methylation | Glide
Journal Article
Astroparticle Physics, ISSN 0927-6505, 2015, Volume 66, pp. 18 - 30
A new hybrid detector system has been constructed by the Tibet ASγ collaboration at Tibet, China, since 2014 to measure the chemical composition of cosmic rays... 
Energy spectrum | Knee | Neural network | Primary mass | Cosmic rays | ASTRONOMY & ASTROPHYSICS | RANGE | PHYSICS, PARTICLES & FIELDS | Neural networks | Analysis | Detectors
Journal Article
Bioorganic & Medicinal Chemistry, ISSN 0968-0896, 06/2019, Volume 27, Issue 12, pp. 2315 - 2322
The insect enzyme GH20 β- -acetyl- -hexosaminidase OfHex1 represents an important chitinolytic enzyme found in the agricultural pest Ostrinia furnacalis... 
MD simulations | OfHex1 | Enzyme inhibitors | β-N-acetyl-d-hexosaminidase | Molecular docking | Glycosyl triazoles | β-N-acetyl-D-hexosaminidase | CHEMISTRY, MEDICINAL | BIOCHEMISTRY & MOLECULAR BIOLOGY | CHEMISTRY, ORGANIC | NAG-THIAZOLINE | beta-N-acetyl-D-hexosaminidase | ACETYL-D-HEXOSAMINIDASE | DYNAMICS | DERIVATIVES | INSIGHTS
Journal Article
Macromolecules, ISSN 0024-9297, 06/2014, Volume 47, Issue 11, pp. 3645 - 3653
We present a systematic approach to characterize the stretching scenarios for dendrimer brushes. We compare mean-field theory for second-generation dendrimer... 
POLYMER SCIENCE | POLYMER BRUSHES | SCALING THEORY | MODEL | DENDRONIZED POLYMERS | ADSORPTION | LAYER
Journal Article
7. Full Text Exploring the binding mechanisms of MIF to CXCR2 using theoretical approachesElectronic supplementary information (ESI) available: Table S1 Binding free energy contributions of the key binding-site residues of CXCR2 predicted by the binding energy decomposition (kcal mol−1). Table S2 Binding free energy contributions of the key binding-site residues of MIF predicted by the binding energy decomposition (kcal mol−1). Table S3 Binding free energy contributions of the key binding-site residues of CXCR2 in the mutated complex predicted by the binding energy decomposition (kcal mol−1). Fig. S1 Sequence alignment of CXCR2 (residues 1-339) and CXCR4 (PDB ID: 3ODU) used for homology modeling. Fig. S2 MD simulation box of the MIF-CXCR2 complex, the lipid and water molecules. There are 125 121 atoms in the simulation box (Model I was chosen to represent). Fig. S3 The Ramachandran plot of CXCR2 constructed by homology modeling. Fig. S4 Comparison of the complex structure predicted by the protein-protein docking (ribbon colored in gray) and the conformation after the last 20 ns MD trajectory (ribbon colored in green). The arrow indicates the movement of TM1, TM4 and TM5. Fig. S5 Schematic depiction of the major interactions of the averaged structure of MIF-CXCR2 over the last 10 ns MD trajectory (generated by the LIGPLOT program). (a) and (b) represent residues 1 to 57 and 58 to 114 of MIF respectively. Fig. S6 Schematic depiction of the major interactions of the averaged structure of the R11A/D44A mutant of MIF with CXCR2 over the last 10 ns MD trajectory (generated by the LIGPLOT program). (a) and (b) represent residues 1 to 57 and 58 to 114 of MIF respectively. See DOI: 10.1039/c4cp05095a
ISSN 1463-9076, 1/2015, Volume 17, Issue 5, pp. 337 - 3382
Macrophage migration inhibitory factor (MIF) is a multi-functional protein that acts as a cytokine and as an enzyme. Recently, MIF was identified as a... 
Journal Article
Macromolecules, ISSN 0024-9297, 09/2010, Volume 43, Issue 18, pp. 7845 - 7851
Off-lattice molecular dynamics simulations are carried out to study fully charged polyelectrolyte brushes with salt, and a comparison with an off-lattice... 
MOLECULAR-DYNAMICS | POLYMER SCIENCE | POLYMER BRUSHES | SURFACE | SCALING THEORY | ADSORPTION | LAYER
Journal Article
by Wang, FF and Xu, XJ
BIOPHYSICAL JOURNAL, ISSN 0006-3495, 02/2019, Volume 116, Issue 3, pp. 353A - 353A
Conference Proceeding
Desalination, ISSN 0011-9164, 11/2018, Volume 445, pp. 1 - 5
Static experiment simulated LT-MED seawater desalination condition was performed to measure antiscale efficiency of polyacrylic acid with a series of molecular... 
MD simulation | Antiscale mechanism | Molecular weight effect | Critical nucleus | LT-MED desalination | ENGINEERING, CHEMICAL | ACID | WATER RESOURCES | SCALE | ADSORPTION | Aquatic resources | Information management | Saline water conversion | Analysis | Sea-water
Journal Article
by Roth, Gregory A., MD, MPH and Johnson, Catherine, PhD and Abajobir, Amanuel, MPH and Abd-Allah, Foad, MD and Abera, Semaw Ferede, MSc and Abyu, Gebre, MS and Ahmed, Muktar, MPH, MBA and Aksut, Baran, MD and Alam, Tahiya, MPH and Alam, Khurshid, PhD and Alla, François, PhD and Alvis-Guzman, Nelson, PhD and Amrock, Stephen, MD and Ansari, Hossein, PhD and Ärnlöv, Johan, PhD and Asayesh, Hamid, PhD and Atey, Tesfay Mehari, MSc and Avila-Burgos, Leticia, PhD and Awasthi, Ashish, MSc and Banerjee, Amitava, DPhil and Barac, Aleksandra, PhD and Bärnighausen, Till, MD and Barregard, Lars, MD and Bedi, Neeraj, MD and Belay Ketema, Ezra, MSc and Bennett, Derrick, PhD and Berhe, Gebremedhin, MPH and Bhutta, Zulfiqar, PhD, MBBS and Bitew, Shimelash, MPH and Carapetis, Jonathan, MBBS, PhD and Carrero, Juan Jesus, PhD and Malta, Deborah Carvalho, MD, PhD and Castañeda-Orjuela, Carlos Andres, MSc and Castillo-Rivas, Jacqueline, MPH and Catalá-López, Ferrán, PhD and Choi, Jee-Young, PhD and Christensen, Hanne, DMSCi and Cirillo, Massimo, MD and Cooper, Leslie, MD and Criqui, Michael, MD, MPH and Cundiff, David, MD and Damasceno, Albertino, PhD and Dandona, Lalit, MD and Dandona, Rakhi, PhD and Davletov, Kairat, MD, PhD, MPH and Dharmaratne, Samath, MD and Dorairaj, Prabhakaran, MD, DM, MSc and Dubey, Manisha, MPhil and Ehrenkranz, Rebecca, MPH and El Sayed Zaki, Maysaa, MD, PhD and Faraon, Emerito Jose A., MD and Esteghamati, Alireza, MD and Farid, Talha, MD and Farvid, Maryam, PhD and Feigin, Valery, PhD and Ding, Eric L., ScD and Fowkes, Gerry, PhD and Gebrehiwot, Tsegaye, MPH and Gillum, Richard, MD and Gold, Audra, MSc and Gona, Philimon, PhD and Gupta, Rajeev, MD, PhD and Habtewold, Tesfa Dejenie, MSc and Hafezi-Nejad, Nima, MD and Hailu, Tesfaye, MBA and Hailu, Gessessew Bugssa, MSc and Hankey, Graeme, MD and Hassen, Hamid Yimam, MPH and Abate, Kalkidan Hassen, MS and Havmoeller, Rasmus, PhD and Hay, Simon I., DSc and Horino, Masako, MPH and Hotez, Peter J., PhD and Jacobsen, Kathryn, PhD and James, Spencer, MD, MPH and Javanbakht, Mehdi, PhD and Jeemon, Panniyammakal, PhD and John, Denny, MBA, MPH and Jonas, Jost, MD and Kalkonde, Yogeshwar, MD and Karimkhani, Chante, MD and Kasaeian, Amir, PhD and Khader, Yousef, ShD and Khan, Abdur, MD and Khang, Young-Ho, MD and Khera, Sahil, MD and Khoja, Abdullah T., MBBS, MPH, MBA and Khubchandani, Jagdish, MBBS, PhD and Kim, Daniel, DrPH and Kolte, Dhaval, MD and Kosen, Soewarta, MD and Krohn, Kristopher J., BA and Kumar, G. Anil, PhD and Kwan, Gene, MD and Lal, Dharmesh Kumar, MD and Larsson, Anders, PhD and Linn, Shai, MD MPH, DrPH and Lopez, Alan, MS, PhD and Lotufo, Paulo A., DrPH and El Razek, Hassan Magdy Abd, MBBCh and ... and Medicinska fakulteten and Medicinska och farmaceutiska vetenskapsområdet and Biokemisk struktur och funktion and Uppsala universitet and Institutionen för medicinska vetenskaper
Journal of the American College of Cardiology, ISSN 0735-1097, 07/2017, Volume 70, Issue 1, pp. 1 - 25
Abstract Background The burden of cardiovascular diseases (CVDs) remains unclear in many regions of the world. Objectives The GBD (Global Burden of Disease)... 
Cardiovascular | Internal Medicine | global health | epidemiology | cause of death | SYSTEMATIC ANALYSIS | CARDIAC & CARDIOVASCULAR SYSTEMS | RISK-FACTORS | COUNTRIES | CAUSE-SPECIFIC MORTALITY | PREVENTION | DISABILITY WEIGHTS | PREVALENCE | TRANSITION | PERIPHERAL ARTERIAL-DISEASE | HYPERTENSION | Morbidity - trends | Risk Assessment - methods | Prevalence | Prospective Studies | Survival Rate - trends | Global Health | Humans | Middle Aged | Risk Factors | Male | Life Expectancy - trends | Young Adult | Cardiovascular Diseases - epidemiology | Sex Distribution | Adult | Cause of Death - trends | Female | Aged | Retrospective Studies | Cardiovascular diseases | Analysis | Heart | Stroke | Life expectancy | Health | Mortality | Cardiovascular disease | Epidemiology | Coronary artery disease | Diseases | Life span | Ischemia | Autopsy | Fatalities | Death | Health risk assessment | Heart diseases | Age | Public health | Index Medicus | Abridged Index Medicus | CVD, cardiovascular disease | IHD, ischemic heart disease | PAD, peripheral arterial disease | RHD, rheumatic heart disease | YLD, years lived with disability | YLL, years of life lost | SDI, sociodemographic index | DALY, disability-adjusted life-year | UI, uncertainty interval | Original Investigation | Medical and Health Sciences | Medicin och hälsovetenskap | Public Health, Global Health, Social Medicine and Epidemiology | Hälsovetenskaper | Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi | Health Sciences
Journal Article
Review of Scientific Instruments, ISSN 0034-6748, 03/2019, Volume 90, Issue 3, pp. 033306 - 033306
The radiochromic film (RCF) is a high-dose, high-dynamic range dosimetry detection medium. A stack of RCFs can be used to detect both spatial and energetic... 
ACCELERATION | INSTRUMENTS & INSTRUMENTATION | PHYSICS, APPLIED | RADIOGRAPHY | Laser plasmas | Dosimeters | Heavy ions | Divergence | Energy spectra | Energy distribution | Calibration | Laser beams | Carbon | Charge distribution | Radiation dosage | Optical density | Ion beams | Lasers | Proton beams
Journal Article
Bioorganic & Medicinal Chemistry, ISSN 0968-0896, 06/2019, Volume 27, Issue 12, p. 2315
The insect enzyme GH20 [beta]-N-acetyl-d-hexosaminidase OfHex1 represents an important chitinolytic enzyme found in the agricultural pest Ostrinia furnacalis... 
Enzyme inhibitors | Triazoles | Agricultural pests
Journal Article
by Yang, B and Lin, SJ and Ren, JY and Liu, T and Wang, YM and Li, CM and Xu, WW and He, YW and Zheng, WH and Zhao, J and Yuan, XH and Liao, HX
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, ISSN 1422-0067, 05/2019, Volume 20, Issue 10, p. 2568
Journal Article
by Kassebaum, Nicholas J, Dr and Bertozzi-Villa, Amelia, BA and Coggeshall, Megan S, BA and Shackelford, Katya A, BA and Steiner, Caitlyn, MPH and Heuton, Kyle R, BS and Gonzalez-Medina, Diego, BA and Barber, Ryan, BS and Huynh, Chantal, BA and Dicker, Daniel, BS and Templin, Tara, BA and Wolock, Timothy M, BA and Ozgoren, Ayse Abbasoglu, MA and Abd-Allah, Foad, Prof and Abera, Semaw Ferede, MSc and Abubakar, Ibrahim, Prof and Achoki, Tom, PhD and Adelekan, Ademola, PhD and Ademi, Zanfina, PhD and Adou, Arsène Kouablan, MD and Adsuar, José C, Prof and Agardh, Emilie E, PhD and Akena, Dickens, PhD and Alasfoor, Deena, MSc and Alemu, Zewdie Aderaw, MPH and Alfonso-Cristancho, Rafael, PhD and Alhabib, Samia, PhD and Ali, Raghib, MSc and Al Kahbouri, Mazin J, PhD and Alla, François, Prof and Allen, Peter J, MPH and AlMazroa, Mohammad A, MD and Alsharif, Ubai, DMD and Alvarez, Elena, PhD and Alvis-Guzmán, Nelson, Prof and Amankwaa, Adansi A, Prof and Amare, Azmeraw T, MPH and Amini, Hassan, MSPH and Ammar, Walid, PhD and Antonio, Carl A T, MD and Anwari, Palwasha, MSc and Ärnlöv, Johan, PhD and Arsenijevic, Valentina S Arsic, Prof and Artaman, Ali, PhD and Asad, Majed Masoud, PhD and Asghar, Rana J, MD and Assadi, Reza, MD and Atkins, Lydia S, MPH and Badawi, Alaa, PhD and Balakrishnan, Kalpana, PhD and Basu, Arindam, PhD and Basu, Sanjay, PhD and Beardsley, Justin, MBChB and Bedi, Neeraj, MD and Bekele, Tolesa, MPH and Bell, Michelle L, Prof and Bernabe, Eduardo, PhD and Beyene, Tariku J, MSC and Bhutta, Zulfiqar, Prof and Bin Abdulhak, Aref, MD and Blore, Jed D, PhD and Basara, Berrak Bora, PhD and Bose, Dipan, PhD and Breitborde, Nicholas, Prof and Cárdenas, Rosario, ScD and Castañeda-Orjuela, Carlos A, MSc and Castro, Ruben Estanislao, PhD and Catalá-López, Ferrán, PhD and Cavlin, Alanur, PhD and Chang, Jung-Chen, Prof and Che, Xuan, PhD and Christophi, Costas A, PhD and Chugh, Sumeet S, Prof and Cirillo, Massimo, Prof and Colquhoun, Samantha M, PhD and Cooper, Leslie Trumbull, MD and Cooper, Cyrus, Prof and da Costa Leite, Iuri, PhD and Dandona, Lalit, Prof and Dandona, Rakhi, PhD and Davis, Adrian, Prof and Dayama, Anand, MD and Degenhardt, Louisa, Prof and De Leo, Diego, Prof and del Pozo-Cruz, Borja, PhD and Deribe, Kebede, MPH and Dessalegn, Muluken, MPH and deVeber, Gabrielle A, MD and Dharmaratne, Samath D, MD and Dilmen, Uğur, MD and Ding, Eric L, ScD and Dorrington, Rob E, MPhil and Driscoll, Tim R, PhD and Ermakov, Sergei Petrovich, Prof and Esteghamati, Alireza, Prof and Faraon, Emerito Jose A, MD and Farzadfar, Farshad, MD and Felicio, Manuela Mendonca, MD and Fereshtehnejad, Seyed-Mohammad, MD and de Lima, Graça Maria Ferreira, BSC and ... and Högskolan Dalarna and Akademin Utbildning, hälsa och samhälle and Medicinsk vetenskap
The Lancet, ISSN 0140-6736, 2014, Volume 384, Issue 9947, pp. 980 - 1004
Journal Article