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1. Full Text Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
by Wu, Guosheng and Robertson, Daniel H and Brooks, Charles L and Vieth, Michal
Journal of Computational Chemistry, ISSN 0192-8651, 10/2003, Volume 24, Issue 13, pp. 1549 - 1562
The influence of various factors on the accuracy of protein‐ligand docking is examined. The factors investigated include the role of a grid representation of... 
CDOCKER | grid approximations | CHARMm | value | MD docking | p value | Grid approximations | SEARCH | FLEXIBILITY | AUTOMATED DOCKING | SIMULATION | CHEMISTRY, MULTIDISCIPLINARY | PREDICTION | ENERGY MINIMIZATION | DATABASE | PROTEIN-LIGAND INTERACTIONS | INHIBITORS | FLEXIBLE DOCKING | Thermodynamics | Algorithms | Computer Simulation | Models, Molecular | Protein Binding | Ligands | Molecular Structure | Proteins - chemistry | Index Medicus
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2. Full Text Automated docking screens: A feasibility study
by Irwin, John J and Shoichet, Brian K and Mysinger, Michael M and Huang, Niu and Colizzi, Francesco and Wassam, Pascal and Cao, Yiqun
Journal of Medicinal Chemistry, ISSN 0022-2623, 09/2009, Volume 52, Issue 18, pp. 5712 - 5720
Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make... 
CHEMISTRY, MEDICINAL | LEAD DISCOVERY | STRUCTURE-BASED DISCOVERY | HIGH-THROUGHPUT | BETA-LACTAMASE | PROTEIN-LIGAND DOCKING | RECEPTOR LIGANDS | DRUG DESIGN | SCORING FUNCTIONS | MOLECULAR DOCKING | FLEXIBLE DOCKING | Drug Evaluation, Preclinical - methods | Automation | Reproducibility of Results | Proteins - metabolism | Databases, Protein | Models, Molecular | Benchmarking | Crystallography, X-Ray | Ligands | Protein Conformation | Proteins - chemistry | Feasibility Studies | Index Medicus
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3. Full Text Study of the interactions of bovine serum albumin with the new anti-inflammatory agent 4-(1,3-dsioxo-1,3-dihydro-2H-isoindol-2-yl)-N-[(4-ethoxy-phenyl) methylidene]benzohydrazide using a multi-spectroscopic approach and molecular docking
by Wani, Tanveer A and Bakheit, Ahmed H and Al-Majed, Abdul-Rahman A and Bhat, Mashooq A and Zargar, Seema
Molecules, ISSN 1420-3049, 08/2017, Volume 22, Issue 8, p. 1258
The lipophilic derivative of thalidomide (4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-N'-[(4-ethoxyphenyl)methylidene] benzohydrazide, 6P) was synthesized to... 
BSA | Lipophilic thalidomide derivative | HSA | Fluorescence | Serum albumin | Thalidomide | Quenching | CARRAGEENAN | PROTEIN | ANALOGS | BIOCHEMISTRY & MOLECULAR BIOLOGY | INJURY | NECROSIS-FACTOR-ALPHA | serum albumin | CHEMISTRY, MULTIDISCIPLINARY | thalidomide | fluorescence | quenching | lipophilic thalidomide derivative | Thermodynamics | Animals | Anti-Inflammatory Agents - chemistry | Cattle | Phthalimides - chemistry | Serum Albumin, Bovine - chemistry | Molecular Docking Simulation | Kinetics | Spectrum Analysis | Hydrazones - chemistry | Bovine serum albumin | Complex formation | Immunomodulation | Van der Waals forces | Enthalpy | Inflammation | Hydrogen bonding | Quenching (cooling) | Studies | Lipophilic | Chemical bonds | Docking | Spectrofluorimetry | Spectrophotometry | Bonding | Binding sites | Index Medicus
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4. Full Text Synthesis, antileishmanial activity and docking study of N′-substitutedbenzylidene-2-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)acetohydrazides
by Sangshetti, Jaiprakash N and Shaikh, Rehan I and Khan, Firoz A. Kalam and Patil, Rajendra H and Marathe, Sayali D and Gade, Wasudev N and Shinde, Devanand B
Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, 03/2014, Volume 24, Issue 6, pp. 1605 - 1610
A series of ′-substitutedbenzylidene-2-(6,7-dihydrothieno[3,2- ]pyridin-5(4 )-yl)acetohydrazide derivatives is synthesized and evaluated for antileishmanial... 
Thieno[3,2-c]pyridine | Antimicrobial activity | Docking study | ADME properties | Antileishmanial activity | L. donovani promastigotes | CHEMISTRY, MEDICINAL | ONE-POT SYNTHESIS | ANALOGS | SENSITIVITY | CHEMISTRY, ORGANIC | CHEMOTHERAPY | DISCOVERY | Thieno[3,2-c] pyridine | ANTICONVULSANT ACTIVITY | BIOLOGICAL EVALUATION | ANTIFUNGAL AGENTS | VISCERAL LEISHMANIASIS | DERIVATIVES | Oxidoreductases - antagonists & inhibitors | Protein Structure, Tertiary | Hydrazines - pharmacology | Oxidoreductases - metabolism | Administration, Oral | Leishmania donovani - drug effects | Protozoan Proteins - antagonists & inhibitors | Pyridines - chemistry | Anti-Infective Agents - pharmacology | Half-Life | Hydrazines - pharmacokinetics | Leishmania donovani - enzymology | Antiprotozoal Agents - pharmacology | Benzylidene Compounds - chemistry | Anti-Infective Agents - chemical synthesis | Microbial Sensitivity Tests | Hydrazines - chemistry | Antiprotozoal Agents - pharmacokinetics | Protozoan Proteins - metabolism | Anti-Infective Agents - pharmacokinetics | Drug Design | Antiprotozoal Agents - chemical synthesis | Molecular Docking Simulation | Binding Sites | Index Medicus
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5. Full Text Quantum mechanical and spectroscopic (FT-IR, FT-Raman) study, NBO analysis, HOMO-LUMO, first order hyperpolarizability and molecular docking study of methyl[(3R)-3-(2-methylphenoxy)-3-phenylpropyl]amine by density functional method
by Kuruvilla, Tintu K and Prasana, Johanan Christian and Muthu, S and George, Jacob and Mathew, Sheril Ann
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, 01/2018, Volume 188, pp. 382 - 393
Quantum chemical techniques such as density functional theory (DFT) have become a powerful tool in the investigation of the molecular structure and vibrational... 
FT-IR | DFT | FT-Raman | Molecular docking | HOMO-LUMO | Anti-depressant | Density functionals | Amines | Antidepressants | Analysis | Methods | Force and energy | Thermodynamics | Raman spectroscopy
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6. Full Text Bufadienolides from Kalanchoe daigremontiana as thrombin inhibitors—In vitro and in silico study
by Kolodziejczyk-Czepas, Joanna and Sieradzka, Malgorzata and Moniuszko-Szajwaj, Barbara and Pecio, Łukasz and Ponczek, Michal B and Nowak, Pawel and Stochmal, Anna
International Journal of Biological Macromolecules, ISSN 0141-8130, 06/2017, Volume 99, pp. 141 - 150
Thrombin is an active plasma coagulation factor II, critical for the formation of fibrin clot during blood coagulation. For that reason, this protein is also a... 
Thrombin | Bufadienolide | Inhibitor | POLYMER SCIENCE | CHEMISTRY, APPLIED | BIOCHEMISTRY & MOLECULAR BIOLOGY | Kalanchoe - chemistry | Thrombin - antagonists & inhibitors | Protease Inhibitors - chemistry | Protease Inhibitors - metabolism | Protease Inhibitors - pharmacology | Proteolysis - drug effects | Bufanolides - metabolism | Thrombin - chemistry | Computer Simulation | Amides - chemistry | Amides - metabolism | Protein Conformation | Bufanolides - chemistry | Bufanolides - pharmacology | Molecular Docking Simulation | Thrombin - metabolism | Hydrolysis | Fibrin | Analysis | Crystals | Physiological aspects | Prothrombin | Structure | Index Medicus
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7. Full Text Protein–ligand docking using FFT based sampling: D3R case study
by Padhorny, Dzmitry and Hall, David R and Mirzaei, Hanieh and Mamonov, Artem B and Moghadasi, Mohammad and Alekseenko, Andrey and Beglov, Dmitri and Kozakov, Dima
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 1/2018, Volume 32, Issue 1, pp. 225 - 230
Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have... 
FFT sampling | Chemistry | Drug design data resource | D3R | Protein ligand docking | Physical Chemistry | Animal Anatomy / Morphology / Histology | Computer Applications in Chemistry | BIOCHEMISTRY & MOLECULAR BIOLOGY | CAPRI | POTENTIALS | PREDICTION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | AFFINITY | TEST SET | SCORING FUNCTIONS | WEB SERVER | Case studies | Computer-aided design | Peptides | Analysis | Biomedical engineering | Proteins | Monte Carlo method | Fourier transforms | Computer simulation | Docking | Ligands | Grid refinement (mathematics) | Fast Fourier transformations | Index Medicus
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8. Full Text Density functional theory/B3LYP study of nanometric 4‐(2,4‐dihydroxy‐5‐formylphen‐1‐ylazo)‐N‐(4‐methylpyrimidin‐2‐yl)benzenesulfonamide complexes: Quantitative structure–activity relationship, docking, spectral and biological investigations
by Saad, Fawaz A and Elghalban, Marwa G and El‐Metwaly, Nashwa M and El‐Ghamry, Hoda and Khedr, Abdalla M
Applied Organometallic Chemistry, ISSN 0268-2605, 10/2017, Volume 31, Issue 10, pp. e3721 - n/a
New metal ion complexes were isolated after coupling with 4‐(2,4‐dihydroxy‐5‐formylphen‐1‐ylazo)‐ N ‐(4‐methylpyrimidin‐2‐yl)benzenesulfonamide (H 2 L) drug... 
spectral characterization | docking | nanometre complexes | azodye | antitumour and antimicrobial studies | QSAR | CU(II) | CU-II | CO(II) | THERMAL-DECOMPOSITION | MOLECULAR DOCKING | NI(II) | CHEMISTRY, INORGANIC & NUCLEAR | COPPER(II) COMPLEXES | AZO | CHROMIUM(III) | II COMPLEXES | CHEMISTRY, APPLIED | Fungicides | Metals | Liver | Iron | Ion distribution | Electron spin | Coupling (molecular) | Fungi | Bacteria | Docking | Coordination compounds | Metal ions | Cadmium | Chemical precipitation | Thermal decomposition | Magnetic resonance | Magnetic moments | Spectra | Bactericides | Nitrogen | Electron microscopy | Investigations | Transmission electron microscopy | Chromium | Ligands | Nickel | Electron paramagnetic resonance
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9. Full Text A Molecular Dynamics–Shared Pharmacophore Approach to Boost Early‐Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator‐Activated Receptor α
by Perricone, Ugo and Wieder, Marcus and Seidel, Thomas and Langer, Thierry and Padova, Alessandro and Almerico, Anna Maria and Tutone, Marco
ChemMedChem, ISSN 1860-7179, 08/2017, Volume 12, Issue 16, pp. 1399 - 1407
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the... 
dynamic pharmacophores | molecular docking | virtual screening | PPARα | drug design | Protein Structure, Tertiary | Area Under Curve | Humans | Crystallography, X-Ray | Molecular Dynamics Simulation | Drug Design | Protein Binding | Ligands | ROC Curve | Molecular Docking Simulation | PPAR alpha - metabolism | Binding Sites | PPAR alpha - chemistry | CHEMISTRY, MEDICINAL | MODULATORS | PPAR alpha | IDENTIFICATION | P-GLYCOPROTEIN | IN-VITRO | POTENT | NITRILE | DRUGS | BIOLOGICAL EVALUATION | PHARMACOLOGY & PHARMACY | MULTIDRUG-RESISTANCE | CATHEPSIN-K INHIBITORS | Index Medicus
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10. Full Text Synthesis, characterization and interaction studies of 1,3,4-oxadiazole derivatives of fatty acid with human serum albumin (HSA): A combined multi-spectroscopic and molecular docking study
by Laskar, Khairujjaman and Alam, Parvez and Khan, Rizwan Hasan and Rauf, Abdul
European Journal of Medicinal Chemistry, ISSN 0223-5234, 10/2016, Volume 122, pp. 72 - 78
An efficient synthesis of fatty acid derivatives of 1,3,4-oxadiazole has been reported and comparative study between conventional heating to that of microwave... 
Microwave irradiation | Spectral studies | Serum albumin | 1,3,4-Oxadiazole | Fatty acid | Molecular docking | DRUG | CHEMISTRY, MEDICINAL | BIOLOGICAL EVALUATION | INHIBITORS | INSIGHT | BINDING | Chemistry Techniques, Synthetic | Oxadiazoles - chemical synthesis | Humans | Protein Binding | Protein Conformation | Molecular Docking Simulation | Oxadiazoles - chemistry | Serum Albumin - chemistry | Spectrum Analysis | Oxadiazoles - metabolism | Serum Albumin - metabolism | Albumin | Islamic schools | Fluorescence | Health savings accounts | Fatty acids | Analysis | Index Medicus
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11. Full Text Synthesis and structure–activity relationship study of novel quinazolinone-based inhibitors of MurA
by Hrast, Martina and Rožman, Kaja and Jukič, Marko and Patin, Delphine and Gobec, Stanislav and Sova, Matej
Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, 08/2017, Volume 27, Issue 15, pp. 3529 - 3533
MurA is an intracellular bacterial enzyme that is essential for peptidoglycan biosynthesis, and is therefore an important target for antibacterial drug... 
Peptidoglycan | MurA enzyme | Quinazolinones | Antibacterial agents | CHEMISTRY, MEDICINAL | PEPTIDOGLYCAN BIOSYNTHESIS | DOCKING | CHEMISTRY, ORGANIC | DISCOVERY | Escherichia coli Infections - drug therapy | Escherichia coli - enzymology | Escherichia coli - drug effects | Humans | Alkyl and Aryl Transferases - metabolism | Enzyme Inhibitors - pharmacology | Alkyl and Aryl Transferases - antagonists & inhibitors | Escherichia coli Infections - microbiology | Structure-Activity Relationship | Enzyme Inhibitors - chemical synthesis | Anti-Bacterial Agents - chemical synthesis | Microbial Sensitivity Tests | Quinazolinones - chemical synthesis | Anti-Bacterial Agents - chemistry | Enzyme Inhibitors - chemistry | Anti-Bacterial Agents - pharmacology | Molecular Docking Simulation | Quinazolinones - chemistry | Quinazolinones - pharmacology | Physiological aspects | Furans | Drug discovery | Drug resistance | Escherichia coli | Index Medicus
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12. Full Text Synthesis of 6,12‐Methanobenzo[d]pyrano[3,4‐g][1,3]dioxocin‐1(12H)‐ones and Study of Their Interaction with DNA and β‐Lactoglobulin
by Sepay, Nayim and Guha, Chayan and Maity, Sanhita and Mallik, Asok K
European Journal of Organic Chemistry, ISSN 1434-193X, 11/2017, Volume 2017, Issue 40, pp. 6013 - 6022
An efficient synthesis of 6,12‐methanobenzo[ d ]pyrano[3,4‐ g ][1,3]dioxocin‐1(12 H )‐ones, a new class of 2,8‐dioxabicyclo[3.3.1]nonanes, starting from... 
Heterocycles | Heterogeneous catalysis | DNA | β‐Lactoglobulin | Binding studies | β-Lactoglobulin | A-TYPE PROANTHOCYANIDINS | ONE-POT | CHEMISTRY, ORGANIC | FLAVONOIDS | MOLECULAR DOCKING | beta-Lactoglobulin | FACILE SYNTHESIS | ALPHA-PYRONES | STEREOSELECTIVE-SYNTHESIS | BINDING-PROPERTIES | PROTEINS | DERIVATIVES
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13. Full Text Design, synthesis, docking study and biological evaluation of some novel tetrahydrochromeno [3′,4′:5,6]pyrano[2,3-b]quinolin-6(7H)-one derivatives against acetyl- and butyrylcholinesterase
by Khoobi, Mehdi and Alipour, Masoumeh and Moradi, Alireza and Sakhteman, Amirhossein and Nadri, Hamid and Razavi, Seyyede Faeze and Ghandi, Mehdi and Foroumadi, Alireza and Shafiee, Abbas
European Journal of Medicinal Chemistry, ISSN 0223-5234, 10/2013, Volume 68, pp. 291 - 300
Novel hybrid derivatives of two known scaffolds; tetrahydroaminoquinoline and coumarin were synthesized and evaluated for both acetylcholinesterase (AChE) and... 
Docking study | Alzheimer's disease | Coumarin | Cholinesterase inhibitor | Tacrine | CHEMISTRY, MEDICINAL | ONE-POT SYNTHESIS | ALZHEIMERS-DISEASE | QUINOLINES | ACETYLCHOLINESTERASE INHIBITORS | COUMARIN DERIVATIVES | Cholinesterase Inhibitors - chemistry | Models, Molecular | Coumarins - chemistry | Cholinesterase Inhibitors - chemical synthesis | Structure-Activity Relationship | Enzyme Activation - drug effects | Benzopyrans - chemistry | Coumarins - pharmacology | Benzopyrans - chemical synthesis | Tacrine - pharmacology | Cholinesterase Inhibitors - pharmacology | Butyrylcholinesterase - metabolism | Drug Design | Inhibitory Concentration 50 | Molecular Docking Simulation | Molecular Structure | Benzopyrans - pharmacology | Binding Sites | Acetylcholinesterase - metabolism | Tacrine - chemistry | Drugstores | Enzymes | Analysis | Index Medicus
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14. Full Text Synthesis, biological evaluation and molecular docking study of N-arylbenzo[d]oxazol-2-amines as potential α-glucosidase inhibitors
by Wang, Jing and Wang, Guangcheng and Peng, Zhiyun and Li, Juan and Li, Xin
Bioorganic & Medicinal Chemistry, ISSN 0968-0896, 11/2016, Volume 24, Issue 21, pp. 5374 - 5379
A novel series of -arylbenzo[ ]oxazol-2-amines ( – ) were synthesized and evaluated for their α-glucosidase inhibitory activity. Compounds – , and displayed... 
α-Glucosidase inhibitor | Structure–activity relationship | Molecular docking | Benzoxazole | Enzyme kinetic study | CHEMISTRY, MEDICINAL | EFFICACY | BIOCHEMISTRY & MOLECULAR BIOLOGY | alpha-Glucosidase inhibitor | CHEMISTRY, ORGANIC | ANTICANCER | IN-VITRO EVALUATION | Structure-activity relationship | AGENTS | BENZOXAZOLE DERIVATIVES | NIDDM | Amines - chemistry | Structure-Activity Relationship | Amines - chemical synthesis | Glycoside Hydrolase Inhibitors - chemistry | Glycoside Hydrolase Inhibitors - pharmacology | Oxazoles - chemistry | Dose-Response Relationship, Drug | Glycoside Hydrolase Inhibitors - chemical synthesis | Oxazoles - chemical synthesis | Saccharomyces cerevisiae - enzymology | Molecular Docking Simulation | Molecular Structure | Oxazoles - pharmacology | Amines - pharmacology | alpha-Glucosidases - metabolism | Index Medicus
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