AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Trott, Oleg, Olson, Arthur J.·2010·Journal of Computational Chemistry
Cited by (1,086)
Items 401–500 of 1,086
- Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A ReviewRocco Meli, Garrett M. Morris, Philip Charles Biggin · 2022 · Frontiers in Bioinformatics
- The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug DiscoveryFrancesca Spyrakis, Mostafa H. Ahmed, Alexander S. Bayden, Pietro Cozzini, Andrea Mozzarelli, Glen E. Kellogg · 2017 · Journal of Medicinal Chemistry
- Methods and Applications of In Silico Aptamer Design and ModelingAndrey A. Buglak, Alexey V. Samokhvalov, Anatoly Vitalievich Zherdev, Boris Borisovich Dzantiev · 2020 · International Journal of Molecular Sciences
- Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and DesignHie, Brian, Bryson, Bryan D., Berger, Bonnie · 2020 · Cell Systems
- Machine learning in computational dockingMohamed A. Khamis, Walid E. Gomaa, Walaa Ahmed · 2015 · Artificial Intelligence in Medicine
- The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helixDavid Barneda, Joan Planas-Iglesias, Maria Laura Gaspar, Dariush Mohammadyani, Sunil Prasannan, Dirk Dormann, Gil‐Soo Han, Stephen A. Jesch, George M. Carman, Valerian E. Kagan et al. · 2015 · eLife
- Computational Determination of Potential Inhibitors of SARS-CoV‑2 Main ProteaseSơn Tùng Ngô, Ngoc Quynh Anh Pham, Ly Le, Duc-Hung Pham, Van V. Vu · 2020 · Journal of Chemical Information and Modeling
- Targeted Treatment of Ischemic Stroke by Bioactive Nanoparticle-Derived Reactive Oxygen Species Responsive and Inflammation-Resolving NanotherapiesJichao Yuan, Lanlan Li, Qinghua Yang, Hong Ran, Jie Wang, Kaiyao Hu, Wendan Pu, Jialu Huang, Lan Wen, Linke Zhou et al. · 2021 · ACS Nano
- Application advances of deep learning methods for de novo drug design and molecular dynamics simulationBai, Qifeng, Liu, Shuo, Tian, Yanan, Xu, Tingyang, Banegas‐Luna, Antonio Jesús, Pérez‐Sánchez, Horacio, Huang, Junzhou, Liu, Huanxiang, Yao, Xiaojun · 2022 · WIREs Computational Molecular Science
- Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cationsLibin Ye, Chris Neale, Adnan Sljoka, Brent R. Lyda, Dmitry Pichugin, Nobuyuki Tsuchimura, Sacha Thierry Larda, Régis Pomès, Angel E. Garcı́a, Oliver P. Ernst et al. · 2018 · Nature Communications
- Oxypurinol Directly and Immediately Activates the Drug-Specific T Cells via the Preferential Use of HLA-B*58:01James J Yun, María J. Marcaida, Klara Eriksson, Heidi Jamin, Stefano Fontana, Werner J. Pichler, Daniel Yerly · 2014 · The Journal of Immunology
- Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectivesZhenjiao Du, Jeffrey R. Comer, Yonghui Li · 2023 · TrAC Trends in Analytical Chemistry
- Improving the generalizability of protein-ligand binding predictions with AI-BindAyan Chatterjee, Robin Walters, Zohair Shafi, Omair Shafi Ahmed, Michael Sebek, Deisy Morselli Gysi, Rose Yu, Tina Eliassi‐Rad, Albert-Ĺaszló Barabási, Giulia Menichetti · 2023 · Nature Communications
- Exploring the role of receptor flexibility in structure-based drug discoveryFeixas, Ferran, Lindert, Steffen, Sinko, William, McCammon, J. Andrew · 2014 · Biophysical Chemistry
- Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamaseAbdelmonaem Messaoudi, Hatem Belguith, Jeannette Ben Hamida · 2013 · Theoretical Biology and Medical Modelling
- A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock VinaVsevolod Yu. Tanchuk, Volodymyr O. Tanin, Andriy I. Vovk, Gennady I. Poda · 2015 · Chemical Biology & Drug Design
- Molecular Dynamics Simulations of the Interactions between Glial Cell Line-Derived Neurotrophic Factor Family Receptor GFRα1 and Small-Molecule LigandsLarisa B. Ivanova, Jaana Tammiku‐Taul, Alfonso T. García‐Sosa, Yulia A. Sidorova, Märt Saarma, Mati M. Karelson · 2018 · ACS Omega
- Pyrazoles and Pyrazolines as Anti-Inflammatory AgentsM. Mantzanidou, Eleni A. Pontiki, Dimitra Hadjipavlou‐Litina · 2021 · Molecules
- Synthesis and inhibition profiles of N-benzyl- and N-allyl aniline derivatives against carbonic anhydrase and acetylcholinesterase – A molecular docking studyIbadulla Mahmudov, Yeliz Demir, Yusuf Sert, Yusif Abdullayev, Afsun R. Sujayev, Saleh Hamad Alwasel, İlhami Gülçın · 2021 · Arabian Journal of Chemistry
- Adenylate cyclase activity of TIR1/AFB auxin receptors in plantsLinlin Qi, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hoermayer, Scott A. Sinclair, Minxia Zou, Charo I. del Genio, Martin Kubeš, Richard Napier, Krzysztof Jaworski et al. · 2022 · Nature
- Structural basis for odorant recognition of the insect odorant receptor OR-Orco heterocomplexYidong Wang, Liang Qiu, Bing Wang, Zeyuan Guan, Zhi Dong, Jie Zhang, Song Cao, Lulu Yang, Bo Wang, Zhou Gong et al. · 2024 · Science
- Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo ConformationsDaniel Seeliger, Bert L. de Groot · 2010 · PLoS Computational Biology
- Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental BioactivityBahareh Honarparvar, Thavendran Govender, Glenn E. M. Maguire, Mahmoud E. S. Soliman, Hendrik Gerhardus Kruger · 2013 · Chemical Reviews
- Discovery of non-squalene triterpenesHui Tao, Lukas Lauterbach, Guangkai Bian, Rong Chen, Anwei Hou, Takahiro Mori, Shu Cheng, Ben Hu, Li Lü, Xin Mu et al. · 2022 · Nature
- Application of Computational Biology and Artificial Intelligence in Drug DesignYue Zhang, Mengqi Luo, Peng Wu, Song Wu, Tzong-Yi Lee, Chen Bai · 2022 · International Journal of Molecular Sciences
- Laccase Activation in Deep Eutectic SolventsMariah L. Toledo, Matheus Mendonça Pereira, Mara G. Freire, João Paulo Alves Silva, João A. P. Coutinho, Ana P. M. Tavares · 2019 · ACS Sustainable Chemistry & Engineering
- Ivermectin Docks to the SARS-CoV-2 Spike Receptor-binding Domain Attached to ACE2Steven P. Lehrer, Peter H. Rheinstein · 2020 · In Vivo
- Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MMVikram Dalal, Poonam Dhankhar, Vishakha Singh, Vishakha Singh, Gaddy Rakhaminov, Dasantila Golemi, Pravindra Kumar · 2021 · The Protein Journal
- Quantum machine learning for chemistry and physicsManas Sajjan, Junxu Li, Raja Selvarajan, Shree Hari Sureshbabu, Sumit Suresh Kale, Rishabh Gupta, Vinit Singh, Sabre Kais · 2022 · Chemical Society Reviews
- Molecular docking and molecular dynamics simulationSakshi Singh, Qanita Bani Baker, Dev Bukhsh Singh · 2021 · Elsevier eBooks
- Novel Cinnamic Acid Derivatives as Antioxidant and Anticancer Agents: Design, Synthesis and Modeling StudiesEleni A. Pontiki, Dimitra Hadjipavlou‐Litina, Κonstantinos E. Litinas, George D. Geromichalos · 2014 · Molecules
- Artificial Intelligence in Aptamer–Target Binding PredictionZihao Chen, Long Hu, Bao‐Ting Zhang, Aiping Lü, Yaofeng Wang, Yuanyuan Yu, Ge Zhang · 2021 · International Journal of Molecular Sciences
- Atomic convolutional networks for predicting protein-ligand binding affinityGomes, Joseph, Ramsundar, Bharath, Feinberg, Evan N., Pande, Vijay S. · 2017 · arXiv
- Potential Natural Compounds for Preventing SARS-CoV-2 (2019-nCoV) InfectionHansen Chen, Qiaohui Du · 2020 · Preprints.org
- Vina-Carb: Improving Glycosidic Angles during Carbohydrate DockingAnita K. Nivedha, David F. Thieker, Spandana Makeneni, Huimin Hu, Robert J. Woods · 2016 · Journal of Chemical Theory and Computation
- Rational Design of in Vivo Tau Tangle-Selective Near-Infrared Fluorophores: Expanding the BODIPY UniversePeter Verwilst, Hye Ri Kim, Jinho Seo, N Sohn, Seung-Yun Cha, Yeongmin Kim, Sungho Maeng, Jung Won Shin, Jong Hwan Kwak, Chulhun Kang et al. · 2017 · Journal of the American Chemical Society
- Study on simultaneous binding of resveratrol and curcumin to β-lactoglobulin: Multi-spectroscopic, molecular docking and molecular dynamics simulation approachesXiaoge Zhang, Yingcong Lu, Ru Song Zhao, Ce Wang, Cuina Wang, Tiehua Zhang · 2021 · Food Hydrocolloids
- AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock VinaMathew R. Koebel, Grant Schmadeke, Richard G. Posner, Suman Sirimulla · 2016 · Journal of Cheminformatics
- Anti-oxidant and anti-inflammatory effects of cinnamaldehyde and eugenol on mononuclear cells of rheumatoid arthritis patientsSomaiya Mateen, Md Tabish Rehman, Sumayya Shahzad, Syed Shariq Naeem, Abul Faiz Faizy, Abdul Qayyum Khan, Mohd Shahnawaz Khan, Fohad Mabood Husain, Shagufta Moin · 2019 · European Journal of Pharmacology
- Functional Characterization and Structural Basis of an Efficient Di- C -glycosyltransferase from Glycyrrhiza glabraMeng Zhang, Fu-Dong Li, Kai Li, Zilong Wang, Yuxi Wang, Jun‐Bin He, Huifei Su, Zhongyi Zhang, Changbiao Chi, Xiaomeng Shi et al. · 2020 · Journal of the American Chemical Society
- Machine‐learning scoring functions for structure‐based drug lead optimizationHongjian Li, Kam‐Heung Sze, Gang Lü, Pedro J. Ballester · 2020 · Wiley Interdisciplinary Reviews Computational Molecular Science
- High affinity truncated aptamers for ultra-sensitive colorimetric detection of bisphenol A with label-free aptasensorMin Jia, Junyi Sha, Zhi‐Hua Li, Wenjing Wang, Hongyan Zhang · 2020 · Food Chemistry
- Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculationSeketoulie Keretsu, Swapnil Pandurang Bhujbal, Seung Joo Cho · 2020 · Scientific Reports
- The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NADJim Sun, Axel Siroy, Ravi K. Lokareddy, Alexander Speer, Kathryn S. Doornbos, Gino Cingolani, Michael Niederweis · 2015 · Nature Structural & Molecular Biology
- Synthesis, biological evaluation and molecular docking of novel series of spiro [(2H,3H) quinazoline-2,1′- cyclohexan]-4(1H)- one derivatives as anti-inflammatory and analgesic agentsKamilia M. Amin, M. M. KAMEL, Manal M. Anwar, Mohammed A. Khedr, Yasmin M. Syam · 2010 · European Journal of Medicinal Chemistry
- Identification and evaluation of bioactive natural products as potential inhibitors of human microtubule affinity-regulating kinase 4 (MARK4)Taj Mohammad, Faez Iqbal Khan, Kevin Alan Lobb, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan · 2018 · Journal of Biomolecular Structure and Dynamics
- A PCBP1–BolA2 chaperone complex delivers iron for cytosolic [2Fe–2S] cluster assemblySarju J. Patel, Avery G. Frey, Daniel J. Palenchar, Sooraj R. Achar, Kimberly B. Zumbrennen‐Bullough, Ajay Amar Vashisht, James Akira Wohlschlegel, Caroline C. Philpott · 2019 · Nature Chemical Biology
- In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2Balaji Gowrivel Vijayakumar, Deepthi Ramesh, Annu Joji, Jayadharini Jayachandra prakasan, Tharanikkarasu Kannan · 2020 · European Journal of Pharmacology
- A Comprehensive Insight into Binding of Hippuric Acid to Human Serum Albumin: A Study to Uncover Its Impaired Elimination through HemodialysisNida Zaidi, Mohammad Rehan Ajmal, Gulam Rabbani, Ejaz Ahmad, Rizwan Hasan Khan · 2013 · PLoS ONE
- Deep Learning and Virtual Drug ScreeningKristy A. Carpenter, David S Cohen, Juliet T. Jarrell, Xudong Huang · 2018 · Future Medicinal Chemistry
- Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule DockingUte F. Röhrig, Mathilde Goullieux, Marine Bugnon, Vincent Zoete · 2023 · Journal of Chemical Information and Modeling
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial reviewMadhuchhanda Mohanty, Priti S. Mohanty · 2023 · Monatshefte für Chemie - Chemical Monthly
- Receptor-based virtual screening protocol for drug discoveryNuno M. F. S. A. Cerqueira, Diana Gesto, Eduardo F. Oliveira, Diogo Santos‐Martins, Natércia F. Brás, Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos · 2015 · Archives of Biochemistry and Biophysics
- Predicting Relative Protein Affinity of Novel Per- and Polyfluoroalkyl Substances (PFASs) by An Efficient Molecular Dynamics ApproachCheng, Weixiao, Ng, Carla A. · 2018 · Environmental Science & Technology
- Diosgenin from Dioscorea bulbifera: Novel Hit for Treatment of Type II Diabetes Mellitus with Inhibitory Activity against α-Amylase and α-GlucosidaseSougata Ghosh, Piyush A. More, Abhishek Derle, Ajay Bhagwan Patil, Pramod R. Markad, Adersh Asok, Navanath Kumbhar, Mahemud L. Shaikh, Ramanamurthy Boppana, Vaishali Shinde et al. · 2014 · PLoS ONE
- In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main ProteaseTien Huynh, Haoran Wang, Binquan Luan · 2020 · The Journal of Physical Chemistry Letters
- Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysisSatyam Kumar Singh, Md Fulbabu Sk, Avinash Sonawane, Parimal Kar, Sushabhan Sadhukhan · 2020 · Journal of Biomolecular Structure and Dynamics
- Design, synthesis, pharmacological evaluation, QSAR analysis, molecular modeling and ADMET of novel donepezil–indolyl hybrids as multipotent cholinesterase/monoamine oxidase inhibitors for the potential treatment of Alzheimer's diseaseÓscar M. Bautista‐Aguilera, Gerard Esteban, Irene Bolea, Katarina M. Nikolic, Danica Agbaba, Ignacio Moraleda, Isabel Iriepa, Abdelouahid Samadi, Elena Soriano, Mercedes Unzeta et al. · 2014 · European Journal of Medicinal Chemistry
- Structure-Based Discovery of the Novel Antiviral Properties of Naproxen against the Nucleoprotein of Influenza A VirusNathalie Lejal, Bogdan Tarus, Edwige Bouguyon, Sylvie Chenavas, Nicolas Bertho, Bernard Delmas, Rob W. H. Ruigrok, Carmelo Di Primo, Anny Slama‐Schwok · 2013 · Antimicrobial Agents and Chemotherapy
- Molecular Mechanisms of Oxygen Activation and Hydrogen Peroxide Formation in Lytic Polysaccharide MonooxygenasesBinju Wang, Paul H. Walton, Carme Rovira · 2019 · ACS Catalysis
- Genomic basis of European ash tree resistance to ash dieback fungusJonathan Stocks, Carey L. Metheringham, William J. Plumb, Steve J. Lee, Laura J. Kelly, Richard A. Nichols, Richard J. A. Buggs · 2019 · Nature Ecology & Evolution
- Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlookAnil Kumar Singh, Muhammad Bilal, Hafiz M.N. Iqbal, Abhay Raj · 2021 · The Science of The Total Environment
- A Combination of Doxycycline and Ribavirin Alleviated Chikungunya InfectionHussin A. Rothan, Hirbod Bahrani, Zulqarnain Mohamed, Teow Chong Teoh, Esaki Muthu Shankar, Noorsaadah Abd Rahman, Rohana Yusof · 2015 · PLoS ONE
- Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza BungeGuanghong Cui, Lixin Duan, Baolong Jin, Jun Qian, Zheyong Xue, Guoan Shen, Hugh Snyder John, Jingyuan Song, Shilin Chen, Luqi Huang et al. · 2015 · PLANT PHYSIOLOGY
- Structure and function of an insect α-carboxylesterase (α Esterase 7) associated with insecticide resistanceColin J. Jackson, Jianwei Liu, Paul D. Carr, Faisal Younus, Chris W. Coppin, Tamara Meirelles, Mathilde Lethier, Gunjan Pandey, David L. Ollis, Robyn J. Russell et al. · 2013 · Proceedings of the National Academy of Sciences
- Donepezil + propargylamine + 8-hydroxyquinoline hybrids as new multifunctional metal-chelators, ChE and MAO inhibitors for the potential treatment of Alzheimer's diseaseLi Wang, Gerard Esteban, Masaki Ojima, Óscar M. Bautista‐Aguilera, Tsutomu Inokuchi, Ignacio Moraleda, Isabel Iriepa, Abdelouahid Samadi, Moussa B. H. Youdim, Alejandro Romero et al. · 2014 · European Journal of Medicinal Chemistry
- Binding of DNA with Rhodamine B: Spectroscopic and molecular modeling studiesMd. Maidul Islam, Maharudra Chakraborty, Prateek Pandya, Abdulla Al Masum, Neelima Gupta, Subrata Mukhopadhyay · 2013 · Dyes and Pigments
- Comprehensive Survey of Recent Drug Discovery Using Deep LearningJintae Kim, Sera Park, Dongbo Min, Wankyu Kim · 2021 · International Journal of Molecular Sciences
- Multifunctional biocatalyst for conjugate reduction and reductive aminationThomas W. Thorpe, James R. Marshall, Vanessa Harawa, Rebecca E. Ruscoe, Aníbal Cuetos, James D. Finnigan, Antonio Angelastro, Rachel S. Heath, Fabio Parmeggiani, Simon J. Charnock et al. · 2022 · Nature
- CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring FunctionsRichard D. Smith, James B. Dunbar, Peter M.U. Ung, Emilio Xavier Esposito, Chao‐Yie Yang, Shaomeng Wang, Heather A. Carlson · 2011 · Journal of Chemical Information and Modeling
- GAMESS As a Free Quantum-Mechanical Platform for Drug ResearchYuri Alexeev, Michael P. Mazanetz, Osamu Ichihara, Dmitri G. Fedorov · 2012 · Current Topics in Medicinal Chemistry
- Drug Repurposing Screening Identifies Tioconazole as an ATG4 Inhibitor that Suppresses Autophagy and Sensitizes Cancer Cells to ChemotherapyPei‐Feng Liu, Kun-Lin Tsai, Chien‐Jen Hsu, Wei-Lun Tsai, Jin‐Shiung Cheng, Hsueh‐Wei Chang, Chung‐Wai Shiau, Yih-Gang Goan, Ho‐Hsing Tseng, Chih-Hsuan Wu et al. · 2017 · Theranostics
- Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug DesignShaherin Basith, Minghua Cui, Stephani Joy Y. Macalino, Jongmi Park, Nina Abigail B. Clavio, Soosung Kang, Sun Choi · 2018 · Frontiers in Pharmacology
- Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual ScreeningTatiana F. Vieira, Sérgio Filipe Sousa · 2019 · Applied Sciences
- A Gram-negative-selective antibiotic that spares the gut microbiomeKristen A. Muñoz, Rebecca J. Ulrich, Archit Kumar Vasan, Matt Sinclair, Po‐Chao Wen, Jessica R. Holmes, Hyang Yeon Lee, Chien‐Che Hung, Christopher J. Fields, Emad Tajkhorshid et al. · 2024 · Nature
- Novel tacrine-coumarin hybrids linked to 1,2,3-triazole as anti-Alzheimer’s compounds: In vitro and in vivo biological evaluation and docking studyZahra Najafi, Mohammad Reza Mahdavi, Mina Saeedi, Elahe Karimpour‐Razkenari, Najmeh Edraki, Mohammad Sharif Sharifzadeh, Mahnaz Khanavi, Tahmineh Akbarzadeh · 2018 · Bioorganic Chemistry
- In silico Screening and Heterologous Expression of a Polyethylene Terephthalate Hydrolase (PETase)-Like Enzyme (SM14est) With Polycaprolactone (PCL)-Degrading Activity, From the Marine Sponge-Derived Strain Streptomyces sp. SM14Eduardo L. Almeida, Andrés Felipe Carrillo Rincón, Stephen A. Jackson, Alan D. W. Dobson · 2019 · Frontiers in Microbiology
- In silico Methods for Design of Kinase Inhibitors as Anticancer DrugsŽarko Gagić, Dušan Ružić, Nemanja Djoković, Teodora Djikić, Katarina M. Nikolic · 2020 · Frontiers in Chemistry
- D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energiesConor D. Parks, Zied Gaieb, Michael W. Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia B. McGaughey, Richard A. Lewis, Scott D. Bembenek et al. · 2020 · Journal of Computer-Aided Molecular Design
- Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico AnalysisRajaiah Alexpandi, Joelma Freire De Mesquita, Shunmugiah Karutha Pandian, Arumugam Veera Ravi · 2020 · Frontiers in Microbiology
- ω-Hydroxyemodin Limits Staphylococcus aureus Quorum Sensing-Mediated Pathogenesis and InflammationSeth M. Daly, Bradley O. Elmore, J.S. Kavanaugh, Kathleen D. Triplett, Mario Figueroa, Huzefa A. Raja, Tamam El‐Elimat, Heidi A. Crosby, Jon Femling, Nadja B. Cech et al. · 2015 · Antimicrobial Agents and Chemotherapy
- Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling MethodsHongliang Xu, Nannan Yao, Haoran Xu, Tianshi Wang, Guiying Li, Zhengqiang Li · 2013 · International Journal of Molecular Sciences
- DockingApp: a user friendly interface for facilitated docking simulations with AutoDock VinaElena Di Muzio, Daniele Toti, Fabio Polticelli · 2017 · Journal of Computer-Aided Molecular Design
- Evaluation of drug–human serum albumin binding interactions with support vector machine aided online automated dockingFerenc Zsila, Zsolt Bikádi, David Malik, Péter Hári, Imre Pechan, Attila Bérces, Eszter Hazai · 2011 · Bioinformatics
- Rottlerin-induced autophagy leads to the apoptosis in breast cancer stem cells: molecular mechanismsDhruv Kumar, Sharmila Shankar, Rakesh K. Srivastava · 2013 · Molecular Cancer
- New analogs of the clinical complement inhibitor compstatin with subnanomolar affinity and enhanced pharmacokinetic propertiesHongchang Qu, Daniel Ricklin, Hongjun Bai, Hui Chen, Edimara S. Reis, Mateusz Maciejewski, Αποστολία Τζέκου, Robert A. DeAngelis, Ranillo R.G. Resuello, Florea Lupu et al. · 2012 · Immunobiology
- An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 ReceptorNegin Forouzesh, Nikita Mishra · 2021 · Molecules
- Xuanfei Baidu Decoction reduces acute lung injury by regulating infiltration of neutrophils and macrophages via PD-1/IL17A pathwayYuying Wang, Xi Wang, Yixuan Li, Zhifeng Xue, Rui Shao, Lin Li, Yan Zhu, Han Zhang, Jian Yang · 2022 · Pharmacological Research
- Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneumFang Zhu, Timothy W. Moural, Kapil Shah, Subba Reddy Palli · 2013 · BMC Genomics
- Antimicrobial lipopeptide tridecaptin A 1 selectively binds to Gram-negative lipid IIStephen Albert Cochrane, Brandon Findlay, Alireza Bakhtiary, Jeella Z. Acedo, Eva M Rodriguez-Lopez, Pascal Mercier, John C. Vederas · 2016 · Proceedings of the National Academy of Sciences
- Deep Learning for Molecular GenerationYoujun Xu, Kangjie Lin, Shiwei Wang, Lei Wang, Chenjing Cai, Chen Song, Luhua Lai, Jianfeng Pei · 2019 · Future Medicinal Chemistry
- Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screeningOsmair Vital de Oliveira, Gerd Bruno Rocha, Andrew S. Paluch, Luciano Tavares da Costa · 2020 · Journal of Biomolecular Structure and Dynamics
- Artificial Intelligence in Pharmaceutical SciencesMingkun Lu, Jiayi Yin, Qi Zhu, Gaole Lin, Minjie Mou, Fuyao Liu, Ziqi Pan, Nanxin You, Xichen Lian, Fengcheng Li et al. · 2023 · Engineering
- Virtual Screening Algorithms in Drug Discovery: A Review Focused on Machine and Deep Learning MethodsTiago Alves de Oliveira, Michel Pires da Silva, Eduardo Habib Bechelane Maia, Alisson Marques da Silva, Alex Gutterres Taranto · 2023 · Drugs and Drug Candidates
- Bioactive Compounds from Culinary Herbs Inhibit a Molecular Target for Type 2 Diabetes Management, Dipeptidyl Peptidase IVAllyson M. Bower, Luis M. Real Hernandez, Mark A. Berhow, Elvira González de Mejı́a · 2014 · Journal of Agricultural and Food Chemistry
- Quinoline derivatives as possible lead compounds for anti-malarial drugs: Spectroscopic, DFT and MD studyB. Sureshkumar, Yohannan Sheena Mary, Chacko Yohannan Panicker, S. Suma, Stevan Armaković, Sanja J. Armaković, Christian Van Alsenoy, Badiadka Narayana · 2017 · Arabian Journal of Chemistry
- Inhibition of tumor–microenvironment interaction and tumor invasion by small-molecule allosteric inhibitor of DDR2 extracellular domainWhitney R. Grither, Gregory D. Longmore · 2018 · Proceedings of the National Academy of Sciences
- Design, Synthesis, Molecular Modeling, Anticancer Studies, and Density Functional Theory Calculations of 4-(1,2,4-Triazol-3-ylsulfanylmethyl)-1,2,3-triazole DerivativesAdeeb Al-Sheikh Ali, Daoud J. O. Khan, Arshi Naqvi, Fawzia Faleh Al-blewi, Nadjet Rezki, Mohamed Reda Aouad, Mohamed Hagar · 2020 · ACS Omega
- DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand DesignMiguel García-Ortegón, Gregor N. C. Simm, Austin Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado · 2022 · Journal of Chemical Information and Modeling
- AI is a viable alternative to high throughput screening: a 318-target studyThe Atomwise AIMS Program, Izhar Wallach, Denzil Bernard, Kong T. Nguyen, Gregory Ho, Adrian Morrison, Adrian Stecuła, Andreana M. Rosnik, Ann Marie O’Sullivan, Aram Davtyan et al. · 2024 · Scientific Reports