Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
Cited by (1,000)
Items 701–800 of 1,000
- Exploring Cannabinoids as Potential Inhibitors of SARS-CoV-2 Papain-like Protease: Insights from Computational Analysis and Molecular Dynamics SimulationsJamie Holmes, Shahidul M. Islam, Kimberly A. Milligan · 2024 · Viruses
- Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulationGenki Kudo, Takumi Hirao, Ryuhei Harada, Takatsugu Hirokawa, Yasuteru Shigeta, Ryunosuke Yoshino · 2024 · Scientific Reports
- Exploring the structural features of Aspartate Trans Carbamoylase (TtATCase) fromThermus thermophilusHB8 through in silico approaches: a potential drug target for inborn error of pyrimidine metabolismSurekha Kanagarajan, Mutharasappan Nachiappan, Dhamodharan Prabhu, Jayaraman Muthukumaran, Krishna Ramadas, Jeyaraman Jeyakanthan · 2013 · Journal of Biomolecular Structure and Dynamics
- Discovery of New Sites for Drug Binding to the Hypertension‐Related Renin–Angiotensinogen ComplexNatércia F. Brás, Pedro Alexandrino Fernandes, Maria João Ramos · 2013 · Chemical Biology & Drug Design
- Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics SimulationsXavier Laurent, Nicolas Renault, Amaury Farce, Philippe Chavatte, Éric Hénon · 2014 · PLoS Computational Biology
- Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1Ting Shi, Yuhui Han, Weihua Li, Yanlong Zhao, Yaqin Liu, Zhimin Huang, Shaoyong Lu, Jian Zhang · 2013 · Journal of Chemical Information and Modeling
- Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNAClaudio Carra, Francis A. Cucinotta · 2011 · Journal of Molecular Modeling
- Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulationRui Xiong, Xiao-Mei Cai, Jing Wei, Pengyu Y. Ren · 2012 · Journal of Molecular Modeling
- Investigation of interaction of thrombin-binding aptamer with thrombin and prethrombin-2 by simulation of molecular dynamicsD. S. Shcherbinin, Alexander V. Veselovsky · 2013 · BIOPHYSICS
- Design and computational support for the binding stability of a new CCR5/CXCR4 dual tropic inhibitorC. Taylor, Bill R. Miller, Carol A. Parish · 2017 · Journal of Molecular Graphics and Modelling
- Discovery and Identification of Pyrazolopyramidine Analogs as Novel Potent Androgen Receptor AntagonistsLingyan Wang, Tian-Qing Song, Xin Wang, Jiazhong Li · 2018 · Frontiers in Pharmacology
- Identifying selective agonists targeting LXRβ from terpene compounds of alismatis rhizomaChuanjiong Lin, Jianzong Li, Chuanfang Wu, Jinku Bao · 2021 · Journal of Molecular Modeling
- AnIn-SilicoApproach to Evaluate the Inhibitory Potency of Selected Hydroxamic Acid Derivatives on Zinc-Dependent Histone Deacetylase EnzymeRamachandren Dushanan, Samantha Weerasinghe, D. P. Dissanayake, Rajendram Senthilnithy · 2021 · Journal of Computational Biophysics and Chemistry
- Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose predictionOmar Demerdash · 2021 · Journal of Computer-Aided Molecular Design
- Insight on the microscopic binding mechanism of bisphenol compounds (BPs) with transthyretin (TTR) based on multi-spectroscopic methods and computational simulationsMuwei Huang, Xiaomei Huang, Li Yong, Dan Jia, Wangli Miao, Hongyan Liu, Zhongsheng Yi · 2022 · Analytical and Bioanalytical Chemistry
- Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass RepartitioningMarharyta Blazhynska, Emma Goulard Coderc de Lacam, Haochuan Chen, Christophe J. Chipot · 2023 · Journal of Chemical Theory and Computation
- Synthesis, biological activity screening and molecular modeling study of acylaminoacetamide derivativesGüneş Çoban, Fadime Aydın Köse, Petek Ballar, Varol Pabuççuoğlu · 2015 · Medicinal Chemistry Research
- Molecular simulation of the interaction mechanism between CodY protein and DNA in Lactococcus lactisLinchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li · 2018 · Frontiers of Chemical Science and Engineering
- Reductive Activity and Mechanism of Hypoxia- Targeted AGT Inhibitors: An Experimental and Theoretical InvestigationWeinan Xiao, Guohui Sun, Tengjiao Fan, Junjun Liu, Na Zhang, Lijiao Zhao, Rugang Zhong · 2019 · International Journal of Molecular Sciences
- Computational Studies on the Mechanism of Orotidine Monophosphate DecarboxylaseJeehiun Katherine Lee, Dean Joseph Tantillo · 2003 · Advances in physical organic chemistry
- The crystal structue of PDE10A complexed with 2dY.-Y. Huang, Yan-Fa Yu, C. Zhang, L. Guo, D. Wu, H.-B. Luo · 2019 · Worldwide Protein Data Bank
- Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid ReceptorDavid D. L. Minh, David A. Cooper, Bing Xie, Lei Shi · 2025 · Journal of Chemical Theory and Computation
- Hyaluronic acid-silybin conjugate for the preparation of multifunctional, biomimetic, vancomycin-loaded self-assembled polymersomes against bacterial sepsisMohammed Ali Gafar, Calvin Andeve Omolo, Usri H. Ibrahim, Ghazi Elamin, Abdelrahman Tageldin, Eman Elhassan, Eman A. Ismail, Irene Mackraj, Thirumala Govender · 2025 · International Journal of Biological Macromolecules
- Hunting potential SIRT2 inhibitors towards cancer treatment: Drug repurposing, molecular dynamics, and binding energy computationsMahmoud A. A. Ibrahim, Khlood A. A. Abdeljawaad, Alaa H. M. Abdelrahman, Grigory Arzumanyan, Gamal A. H. Mekhemer, Ashraf M. M. Abdelbacki, Peter A. Sidhom, Shaban R. M. Sayed, Mohamed‐Elamir F. Hegazy · 2025 · Biochemical and Biophysical Research Communications
- Revealing the Role of the Arg and Lys in Shifting Paradigm from BTK Selective Inhibition to the BTK/HCK Dual Inhibition - Delving into the Inhibitory Activity of KIN-8194 against BTK, and HCK in the Treatment of Mutated BTKCys481 Waldenström Macroglobulinemia: A Computational ApproachGhazi Elamin, Aimen Aljoundi, Mohamed I. Alahmdi, Nader Elmaghwry Abo-Dya, Mahmoud E. S. Soliman · 2023 · Anti-Cancer Agents in Medicinal Chemistry
- Unraveling the Molecular Basis for G‐Quadruplex‐Binders to ALS/FTD‐Associated G4C2 Repeats of the C9orf72 GeneLuisa D’Anna, Darren Wragg, Daniela Mauro, Simona Rubino, Alessio Terenzi, Giampaolo Barone, Sophie R. Thomas, Angela Casini, Riccardo Bonsignore, Angelo Spinello · 2024 · ChemBioChem
- Identification of the Heptapeptide PR7 and Octapeptide SF8 With Potent Antioxidative and Angiotensin Converting Enzyme Inhibitory Activity From the Fermented Dairy By‐Product “Buttermilk”Osama Magouz, Mahmoud A. A. Ibrahim, N. M. Mehanna, Sabrina Gensberger‐Reigl, Sevim Dalabasmaz, Monika Pischetsrieder · 2024 · Food Frontiers
- A Multifaceted Computational Approach to Identify PAD4 Inhibitors for the Treatment of Rheumatoid Arthritis (RA)Mansour S. Alturki, Mohamed Sayed Gomaa, Nada Tawfeeq, Abdulaziz Hassan Al Khzem, Mohsina Bano, Murtadha Alshaikh Jafar, Mohammad Alsamen, Hasan Al Nahab, Mohammad Al-Eid, Alhassan Almutawah et al. · 2025 · Metabolites
- Energetic differences between non-domain-swapped and domain-swapped chain connectivities in the K2P potassium channel TRAAKCarlos Navarro‐Retamal, Julio Caballero · 2018 · RSC Advances
- Structural and energetic features of the dimerization of the main proteinase of SARS-CoV-2 using molecular dynamic simulationsYunju Zhang, Liangzhen Zheng, Yanmei Yang, Yuanyuan Qu, Yongqiang Li, Mingwen Zhao, Yuguang Mu, Weifeng Li · 2022 · Physical Chemistry Chemical Physics
- Impact of the R292K Mutation on Influenza A (H7N9) Virus Resistance towards Peramivir: A Molecular Dynamics PerspectiveSphamandla E. Mtambo, Samuel Chima Ugbaja, Hezekiel Mathambo Kumalo · 2022 · Molecules
- Multitarget Potential of Phytochemicals from Traditional Medicinal Tree, Terminalia arjuna (Roxb. ex DC.) Wight & Arnot as Potential Medicaments for Cardiovascular Disease: An In-Silico ApproachVikas Kumar, Nitin Sharma, Raha Saud Orfali, Chirag Patel, Radwan A. Alnajjar, Rakshandha Saini, Anuradha Sourirajan, Prem Kumar Khosla, Kamal Dev, Shagufta Perveen · 2023 · Molecules
- Curcumin interferes with chitin synthesis in Aedes aegypti: a computational and experimental investigationPriyashi Rao, Jinal Ninama, Mansi Dudhat, Dweipayan Goswami, Rakesh Rawal · 2023 · Molecular Diversity
- Therapeutic Path to Triple Knockout: Investigating the Pan-inhibitory Mechanisms of AKT, CDK9, and TNKS2 by a Novel 2-phenylquinazolinone Derivative in Cancer Therapy- An In-silico Investigation TherapyXylia Q. Peters, Ghazi Elamin, Aimen Aljoundi, Mohammed Issa Alahmdi, Nader Elmaghwry Abo-Dya, Peter A. Sidhom, Ahmed Mohamed Tawfeek, Mahmoud A. A. Ibrahim, Opeyemi S. Soremekun, Mahmoud E. S. Soliman · 2023 · Current Pharmaceutical Biotechnology
- (-)-5-Demethoxygrandisin B a New Lignan from Virola surinamensis (Rol.) Warb. Leaves: Evaluation of the Leishmanicidal Activity by In Vitro and In Silico ApproachesSteven Souza Paes, João Victor Silva‐Silva, Paulo Wender Portal Gomes, Luely Oliveira da Silva, Ana Paula Lima Costa, Manoel Leão Lopes Júnior, Daiana de Jesús Hardoim, Carla Junqueira Moragas-Tellis, Noemi Nosomi Taniwaki, Álvaro Luiz Bertho et al. · 2023 · Pharmaceutics
- Non-small cell lung cancer sensitisation to platinum chemotherapy via new thiazole-triazole hybrids acting as dual T-type CCB/MMP-9 inhibitorsHassan El Gamal, Khadiga A. Ismail, A-Mohsen M. E. Omar, Mohamed Teleb, Marwa Muhammad Abu-Serie, Sun Huang, Abdallah S. Abdelsattar, Gerald Werner Zamponi, Hesham T. Y. Fahmy · 2024 · Journal of Enzyme Inhibition and Medicinal Chemistry
- The High‐Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin‐Like Protease: Gln192 and Lys218 Are Key DeterminantsBálint Zoltán Németh, Bence Kiss, Miklós Sahin‐Tóth, Csaba Magyar, Gábor Pál · 2024 · Proteins Structure Function and Bioinformatics
- Investigation into mechanism of orotidine 5′-monophosphate decarboxylase enzyme by MM-PBSA/MM-GBSA and molecular dockingShirin Jamshidi, Hashem Rafii‐Tabar, Seifollah Jalili · 2013 · Molecular Simulation
- Identification of novel JMJD2A inhibitor scaffold using shape and electrostatic similarity search combined with docking method and MM-GBSA approachTaotao Feng, Weilin Chen, Dong‐Dong Li, Hongzhi Lin, Fang Liu, Qichao Bao, Yonghua Lei, Xiaojin Zhang, Xiaoli Xu, Xiaoke Guo et al. · 2015 · RSC Advances
- Homology modeling and molecular dynamics simulation studies of human type 1 3β‐hydroxysteroid dehydrogenase: Toward the understanding of cofactor specificityYongbing Zhao, Jingfa Xiao · 2010 · Journal of Computational Chemistry
- Comparative Study on the Binding Affinity of Methimazole and Propylthiouracil to Thyroid Peroxidase as an Anti-Thyroid Drug: An Insilico ApproachSushmita Pradhan, Himakshi Sarma, Barsha Bharadwaz, Venkata Satish Kumar Mattaparthi · 2017 · Journal of Molecular Imaging & Dynamics
- Nonameric Peptide Orchestrates Signal Transduction in the Activating HLA-E/NKG2C/CD94 Immune Complex as Revealed by All-Atom SimulationsEva Prašnikar, Andrej Perdih, Jure Borišek · 2021 · International Journal of Molecular Sciences
- Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulationsPanpan Wang, Xiaonan Gao, Ke Zhang, Qinglan Pei, Xiaobo Xu, Fengmei Yan, Jianghong Dong, Chenxi Jing · 2021 · Physical Chemistry Chemical Physics
- Extending the lore of curcumin as dipteran Butyrylcholine esterase (BChE) inhibitor: A holistic molecular interplay assessmentPriyashi Rao, Dweipayan Goswami, Rakesh Rawal · 2022 · PLoS ONE
- Molecular dynamics approach to probe PKCβII–ligand interactions and influence of crystal water molecules on these interactionsBaljinder K. Grewal, Jyotsna Bhat, Masilamani Elizabeth Sobhia · 2014 · Expert Opinion on Therapeutic Targets
- Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferasesPitchayathida Mee-udorn, Bodee Nutho, Romchalee Chootrakool, Somchart Maenpuen, Ubolsree Leartsakulpanich, P. Chitnumsub, Thanyada Rungrotmongkol · 2022 · Journal of Molecular Liquids
- Biophysical analysis of the putative acetyltransferase SACOL2570 from methicillin-resistant Staphylococcus aureusHai‐Bin Luo, A.A. Knapik, Janusz Jurand Petkowski, Matthew Demas, I.A. Shumilin, Heping Zheng, M. Chruszcz, Wladek Minor · 2013 · Journal of Structural and Functional Genomics
- Theoretical prediction of the binding free energy for mutants of replication protein AClaudio Carra, Janapriya Saha, Francis A. Cucinotta · 2011 · Journal of Molecular Modeling
- Exploring the Pivotal Role of the CK2 Hinge Region Sub-Pocket in Binding with Tricyclic Quinolone Analogues by Computational AnalysisYue Zhou, Na Zhang, Shan Tang, Xiaoqian Qi, Lijiao Zhao, Rugang Zhong, Yongzhen Peng · 2017 · Molecules
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational RestraintsNotari, Evangelia, Wood, Christopher W., Michel, Julien · 2025 · Journal of Chemical Theory and Computation
- Comprehensive analysis of Syzygium cumini L. pomace extract as an α-amylase inhibitor: In vitro inhibition, kinetics, and computational studiesVenkatramanan Varadharajan, Ashwath Kumar Balu, Bruce Joshua Sinclair, Gopi Krishna Perinbarajan, Dharshini Jenifer. A, Harish Ganesan Sudha, Arulvel Ramaswamy, Baskar Venkidasamy, Muthu Thiruvengadam · 2025 · Bioorganic Chemistry
- Discovery of a reversible ALDH1A3 inhibitor through a consensus docking-based virtual screening studyE. Batlle, Raquel Pequerul, Jaume Farrés, Leif Axel Eriksson, Klaus Pors, V. Jha · 2025 · Journal of Computer-Aided Molecular Design
- Exploration of African natural products as VP35 inhibitors to combat Marburg virus infection: Molecular docking, molecular dynamics, and quantum mechanical computationsAlaa H. M. Abdelrahman, Gamal A. H. Mekhemer, Peter A. Sidhom, Mohamed A. El‐Tayeb, Shahzeb Khan, Mahmoud A. A. Ibrahim · 2025 · PLoS ONE
- Insights from integrated covalent docking and molecular dynamics simulations of nirmatrelvir analogs as potential SARS-CoV-2 Mpro inhibitorsMahmoud A. A. Ibrahim, Doaa M. A. Khaled, Doaa G. M. Mahmoud, Alaa H. M. Abdelrahman, Peter A. Sidhom, Yanshuo Han, Tamer Shoeib, Badr Abdullah Aldahmash, Ahmed Moustafa Rady · 2025 · Scientific Reports
- A reversible allosteric inhibitor of GlyT2 for neuropathic pain without on-target side effectsRyan Cantwell Chater, Julian Peiser-Oliver, Tanmay K. Pati, Ada Quinn, Irina Lotsaris, Zachary J. Frangos, Kristen E. Anderson, Anna E. Tischer, Billy J. Williams‐Noonan, Karin R. Aubrey et al. · 2026 · Nature Communications
- Novel benzylidene derivatives: Synthesis and their antimicrobial and anticancer studies and in silico investigationsSarkar M. A. Kawsar, Md. Ahad Hossain, Mohammad I. Hosen, Mehul P. Parmar, Subham G. Patel, Hitendra Mangubhai Patel, Imtiaj Hasan, Suvro Biswas, Md. Abu Saleh · 2024 · Chemical Physics Impact
- Improved Inhibitors Targeting the Thymidylate Kinase of Multidrug-Resistant Mycobacterium tuberculosis with Favorable PharmacokineticsSouleymane Konate, Koffi N’Guessan Placide Gabin Allangba, Issouf Fofana, N’guessan Raymond Kre, Eugène Megnassan, Stanislav Miertuš, Vladimı́r Frecer · 2025 · Life
- Interactions of flavonoid and coumarin derivative compounds with transforming growth factor-beta receptor 1 (TGF-βR1): integrating virtual screening, molecular dynamics, maximum common substructure, and ADMET approaches in the treatment of idiopathic pulmonary fibrosisErman Salih Istıflı, Paulo A. Netz · 2025 · Journal of Molecular Modeling
- Rationalizing the structural basis of organic-platinum hybrid complexes binding towards quadruplex-duplex hybrids through all-atom simulations.Salvatore Muscarella, Irene Treccarichi, Luisa D'Anna, A. Spinello · 2025 · Journal of Inorganic Biochemistry
- In silico study unravels the inhibitory potential of phenolic acids against the Interleukin-6 and TNF-α: Revealing the route to anti-inflammatory effectsPrem Rajak, Abhratanu Ganguly, Sukhendu Dey, Kamalesh Sen, Monojit Banerjee, Arun Mukherjee · 2025 · Food and Humanity
- Discovery of Novel Inhibitors of Aspergillus fumigatus DHODH via Virtual Screening, MD Simulation, and In Vitro Activity AssayKaige Li, Wei Xia, John Z. H. Zhang · 2025 · Molecules
- An Amyloidogenic Fragment of the Spike Protein from SARS-CoV-2 Virus Stimulates the Aggregation and Toxicity of Parkinson’s Disease Protein Alpha-SynucleinJoão Flavio Gemignani, Paulo A. Netz, Daniel Izecksohn, David Dabkiewicz, Ming-Hao Li, Adalgisa Felippe Wiecikowski, David Eliezer, Yraima Cordeiro, Cristian Follmer · 2025 · ACS Chemical Neuroscience
- Drug Repurposing Investigation for Combating Ebola Virus Disease: Database Mining, Docking Calculations, Molecular Dynamics, and Density Functional Theory StudyAlaa H. M. Abdelrahman, Gamal A. H. Mekhemer, Peter A. Sidhom, Mohamed A. El‐Tayeb, Shahzeb Khan, Mahmoud A. A. Ibrahim · 2025 · ChemistryOpen
- Novel 3-phenyl-1- (alkylphenyl)-9-oxa-4-azaphenanthren-10-ones as inhibitors of some enzymes: synthesis, characterization, biological evaluation and molecular docking studiesDonia Bensalah, Ahlem Chakchouk Mtibaa, Lotfi Mellouli, Houcine Ghalla, Waleed Syaed Koko, Sadeq M. Al‐Hazmy, Lamjed A. Mansour, Jameel Al‐Tamimi, Najet Aouled Dlala, Younes Bouazizi et al. · 2022 · Journal of Biomolecular Structure and Dynamics
- Investigation on substrate specificity and catalytic activity of serine protease neuropsinMasami Lintuluoto, Mitsumasa Abe, Yota Horioka, Yoshifumi Fukunishi, Hideki Tamura, Juha Mikael Lintuluoto · 2022 · Biophysics and Physicobiology
- Molecular insights into the interaction of eighteen different variants of SARS-CoV-2 spike proteins with sixteen therapeutically important phytocompounds: in silico approachBhavika Batra, Suchetha Srinivasan, Santhana Gopalakrishnan Gopalakrishnan, Chirag N. Patel, Vikas Kumar, Anuradha Sourirajan, Kamal Dev · 2023 · Journal of Biomolecular Structure and Dynamics
- Loading and co-solvent-triggered release of okanin, a C4 plant key enzyme inhibitor, into/from functional microgelsJonas Dittrich, Fabian Kolodzy, Alexander Töpel, Alexander Hofmann, Georg Groth, Andrij Pich, Holger Gohlke · 2023 · Chemical Engineering Journal
- Insights into the binding mechanism between α‐TOH and CYP4F2: A homology modeling, molecular docking, and molecular dynamics simulation studyLeilei Liang, Qing‐Chuan Zheng · 2023 · Journal of Cellular Biochemistry
- Molecular dynamic simulation reveals the molecular interactions of epidermal growth factor receptor with musk xylene are involved in the carcinogenicityHuaxing Fei, Wen Jing Li, Nan Lü, Qing Huo Liu, Youyu Zhang · 2023 · RSC Advances
- Computational study of SENP1 in cancer by novel natural compounds and ZINC database screeningSomayye Taghvaei, Alireza Taghvaei, Mohammad Saberi Anvar, Chun Guo, Farzaneh Sabouni, Zarrin Minuchehr · 2023 · Frontiers in Pharmacology
- Discovery of novel polyheterocyclic neuraminidase inhibitors with 1,3,4-oxadiazole thioetheramide as core backboneLin Lin Shang, Zhi Jian Zhong, Li Ping Cheng · 2024 · European Journal of Medicinal Chemistry
- Specialized compounds of four Cameroonian spices: Isolation, characterization, and in silico evaluation as prospective SARS-CoV-2 inhibitorsGervais Mouthé Happi, Klev Gaïtan Sikam, Mahmoud A. A. Ibrahim, Liliane Clotilde Dzouemo, Guy-Paulin Mouthé Kemayou, Praid Likane Keuteu, Peter A. Sidhom, Shaban R. M. Sayed, Mohamed‐Elamir F. Hegazy, Jean Duplex Wansi · 2024 · Open Chemistry
- Design, synthesis, and evaluation of quinolin-2(1H)-ones as PDE1 inhibitors for the treatment of inflammatory bowel diseaseQian Zhou, Weihao Luo, Bei Zhang, Zhao-Hang Xue, Qinghua Huang, Lingling Feng, Yinuo Wu, Chen Zhang · 2024 · Bioorganic Chemistry
- Essential oil constituents of regional ethnomedicinal plants as potential inhibitors of SARS-CoV-2 M pro : an integrated molecular docking, molecular dynamics and QM/MM studyAmbalika Phonglo, Dikshita Dowerah, Srutishree Sarma, Najima Ahmed, Priyanka Dutta, Moumita Basumutary, Ramesh C. Deka · 2024 · Journal of Biomolecular Structure and Dynamics
- Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learningErica Teixeira Prates, Omar Demerdash, Manesh B. Shah, Tomás A. Rush, Udaya C. Kalluri, Daniel Jacobson · 2025 · Computational and Structural Biotechnology Journal
- Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum studyVannajan Sanghiran Lee, Kanchanok Kodchakorn, Jitrayut Jitonnom, Piyarat Nimmanpipug, Prachya Kongtawelert, Bhusana Premanode · 2010 · Journal of Computer-Aided Molecular Design
- Modifying Poisson equation for near-solute dielectric polarization and solvation free energyPei‐Kun Yang · 2016 · Chemical Physics
- Elucidating the energetic contributions to the binding free energyMazen Ahmad, Volkhard Helms, Olga V. Kalinina, Thomas Lengauer · 2017 · The Journal of Chemical Physics
- Host-guest interactions between sildenafil and cyclodextrins: Spectrofluorometric study and molecular dynamic modelingTan Suwandecha, Chompoonut Rungnim, Supawadee Namuangruk, Uracha Ruktanonchai, Somchai Sawatdee, Janwit Dechraksa, Teerapol Srichana · 2017 · Journal of Molecular Graphics and Modelling
- The Identification of Potential Human Rhinovirus Inhibitors: Exploring the Binding Landscape of HRV-3C Protease Through PRED Pharmacophore ScreeningNdumiso M. Buthelezi, Kgothatso Eugene Machaba, Mahmoud E. S. Soliman · 2017 · Future Virology
- Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline‐rich tyrosine kinase 2‐beta: Insights from molecular dynamics simulationsEleni Michael, Savvas Polydorides, Vasilis J. Promponas, Paris A. Skourides, Georgios Archontis · 2020 · Proteins Structure Function and Bioinformatics
- MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-MotifAmen Shamim, Maria Razzaq, Kyeong Kyu Kim · 2020 · International Journal of Molecular Sciences
- Biomolecular Talks—Part 1: A Theoretical Revisit on Molecular Modeling and Docking ApproachesAmutha Ramaswamy, Sangeetha Balasubramanian, Muthukumaran Rajagopalan · 2021 · Elsevier eBooks
- Dual‐Inhibition of Human N‐Myristoyltransferase Subtypes Halts Common Cold Pathogenesis: Atomistic Perspectives from the Case of IMP‐1088**Clement Agoni, Elliasu Yakubu Salifu, Gill M. Enslin, Samuel K. Kwofie, Mahmoud E. S. Soliman · 2021 · Chemistry & Biodiversity
- Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approachVenkataraghavan Ragunathan, K. Chithra, C. Shivanika, Meenambiga Setti Sudharsan · 2022 · In Silico Pharmacology
- Versisterol, a new endophytic steroid with 3CL protease inhibitory activity from Avicennia marina (Forssk.) Vierh.Marwa Elsbaey, Mahmoud A. A. Ibrahim, Mohamed‐Elamir F. Hegazy · 2022 · RSC Advances
- Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams · 2022 · Journal of Chemical Information and Modeling
- Binding Modes of Xanthine‐Derived Selective Allosteric Site Inhibitors of MTHFD2Vibhu Jha, Leif Axel Eriksson · 2023 · ChemistryOpen
- Evaluating point-prediction uncertainties in neural networks for protein-ligand binding predictionYa Ju Fan, Jonathan Allen, Kevin McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone · 2023 · Artificial Intelligence Chemistry
- Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics ApproachSushmita Pradhan, Pundarikaksha Das, Venkata Satish Kumar Mattaparthi · 2018 · ACS Omega
- Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolyticaZahra Shahzadi, Ghulam Abbas, Syed Sikander Azam · 2020 · Journal of Molecular Liquids
- Computational Investigation of the Binding Dynamics of Oligo p-Phenylene Ethynylene Fluorescence Sensors and Aβ OligomersTye D. Martin, Gabriella Brinkley, David G. Whitten, Eva Y. Chi, Deborah G. Evans · 2020 · ACS Chemical Neuroscience
- Computer-Aided Drug Discovery: Physics-based Simulations from the Molecular to the Cellular LevelJames Andrew McCammon · 2008 · IMPERIAL COLLEGE PRESS eBooks
- Computation of non-covalent binding affinitiesJames Andrew McCammon · 2005 · Elsevier eBooks
- Mining the Protein Data Bank to improve prediction of changes in protein-protein bindingSamuel Coulbourn Flores, Athanasios Alexiou, Anastasios Glaros · 2021 · PLoS ONE
- The Role of Aspartic Acid 143 in E. coli tRNA-Guanine Transglycosylase: Insights from Mutagenesis Studies and Computational ModelingKatherine Abold Todorov, Xiao-Jian Tan, Susanne T. Nonekowski, George A. Garcia, Heather A. Carlson · 2005 · Biophysical Journal
- Molecular description of α‐keto‐based inhibitors of cruzain with activity against Chagas disease combining 3D‐QSAR studies and molecular dynamicsÁdria P. B. Saraiva, Ricardo Morais de Miranda, Renan Patrick da Penha Valente, Jéssica de Oliveira Araújo, Rutelene N. B. Souza, Clauber Henrique Souza da Costa, Amanda Ruslana Santana Oliveira, Michell O. Almeida, Antônio Florêncio de Figueiredo, João Elias Vidueira Ferreira et al. · 2018 · Chemical Biology & Drug Design
- Molecular Dynamic Investigation of H5N1 Influenza Virus Dual H274Y-I222K Mutation Resistance to PeramivirNdumiso M. Buthelezi, Sphamandla E. Mtambo, Daniel Gyamfi Amoako, Anou Moise Somboro, Elliasu Yakubu Salifu, Rene Bernadette Khan, Ndumiso Nhlakanipho Mhlongo, Hezekiel Mathambo Kumalo · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- New Insights into the Interaction of Sugarcane Cystatin (CaneCPI-5) with the Surface of Hydroxyapatite through Molecular Dynamics SimulationsCarolina Ruis Ferrari, Tiago Espinosa de Oliveira, Flávio Henrique‐Silva, Marília Afonso Rabelo Buzalaf, Paulo A. Netz · 2025 · Caries Research
- Machine Learning-Enabled Insights: Dihydromyricetin’s Novel Role in Inhibiting the TGF-β/ALK5 Signaling Cascade for the Treatment of Pulmonary FibrosisLuyao Dong, Wenting Dong, Yixin Ren, Chunjie Xu, Xiukun Wang, Peiyi Sun, Yao Meng, Congran Li, Guoqing Li, Jian‐Dong Jiang et al. · 2025 · Engineering