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ORCIDJournal of Computer-Aided Molecular Design, Volume 39
Volume 39, Number 1, December 2025
- Jan Blumenstein, Hana Dostálová, Lenka Rucká, Vaclav Stepánek, Tobias Busche, Jörn Kalinowski, Miroslav Pátek, Ivan Barvík
:
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis. 1 - Sophia M. N. Hönig, Torben Gutermuth, Christiane Ehrt, Christian Lemmen, Matthias Rarey:
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays. 2 - Alexander Kensert, Gert Desmet, Deirdre Cabooter:
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras. 3 - Menghan Guo, Zengpeng Li, Xuejin Deng, Ding Luo, Jingyi Yang, Yingjun Chen, Weiwei Xue:
ConoDL: a deep learning framework for rapid generation and prediction of conotoxins. 4 - Siddharth Yadav, Swati Rana, Manish Manish, Sohini Singh, Andrew M. Lynn, Puniti Mathur:
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes. 5 - Fangfang Jiao, Ran Xu, Qing Luo, Xinkang Li, Henry H. Y. Tong, Jingjing Guo:
Elucidating allosteric signal disruption in PBP2a: impact of N146K/E150K mutations on ceftaroline resistance in methicillin-resistant Staphylococcus aureus. 6 - Vincent A. Obakachi, Vaderament-A. Nchiozem-Ngnitedem, Krishna K. Govender, Penny P. Govender:
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry. 7 - Bisma Ishtiaq, Rehan Zafar Paracha, Maryum Nisar, Saima Ejaz, Zamir Hussain:
Discovering promising drug candidates for Parkinson's disease: integrating miRNA and DEG analysis with molecular dynamics and MMPBSA. 8 - Tanya Waseem, Muhammad Kazim Zargaham, Madiha Ahmed, Tausif Ahmed Rajput, Adnan Amin, Humaira Nadeem:
Computational investigation to identify multi-targeted anti-hyperglycemic potential of substituted 2-Mercaptobenzimidazole derivatives and synthesis of new α-glucosidase inhibitors. 9 - Nikita Negi, Senthil R. Ayyannan, Rati K. P. Tripathi:
Multi-targeted benzylpiperidine-isatin hybrids: Design, synthesis, biological and in silico evaluation as monoamine oxidases and acetylcholinesterase inhibitors for neurodegenerative disease therapies. 10 - Momita Rani Baro, Manas Das, Leena Das, Aashis Dutta:
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL. 11 - Vera A. Spanke, Valentin J. Hoerschinger, Veronika Ruzsanyi, Klaus R. Liedl:
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4. 12 - Anuroopa G. Nadh, M. Jitha Kunhikrishnan, Vishal Ravi, Krishnapriya Ramakrishnan, Niyas Rehman, Krishna S. B. Adithya, Amjesh Revikumar, P. R. Sudhakaran, Rajesh Raju:
Convolidine as potent BACE1 inhibitor for Alzheimer's disease; in-silico coupled with in-vitro assessment. 13 - N. Madadi Mahani, H. Hamidian, S. Fozooni, M. Salajeghe:
Synthesis, TD-DFT calculations, molecular docking and ADME studies of new spiro-oxindole derivatives containing 5(4H)-oxazolone as anti-viral and anti-bacterial agents. 14 - Hammad Ahmad, Ashraf Ullah Khan, Waqas Alam, Hany W. Darwish, Abdul Saboor Pirzada, Haroon Ahmed Khan:
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models. 15 - Akansha Pandit, Shubham Srivastava, Neeraj Kumar, Devesh M. Sawant:
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics. 16 - Sara M. Ahmed, Elham Ali, Amina R. Ali, Mona A. Mohamed, Hemmat Mansour Abdelhafez, Alya Mashaal:
MiR-146/TNF-α/IL-6/osteocalcin crosstalk in anti-rheumatic potential of Galleria mellonella hemolymph from computational molecular modeling to in-vivo validation. 17 - Yue Peng, Zilong Li, Yunyi Zhang, Haiyang Ye, Li Mei, Shuyong Shang, Peng Zhou:
Rational molecular design of novel class-III peptidic antagonists to competitively disrupt human PPARδ self-binding peptide. 18 - Padmanabhan Anbazhagan, Jothi Anantharajan, Justina Fulwood, Choon Heng Low, Nithya Baburajendran, Klement Foo, Weijun Xu:
Structure-based discovery of novel non-covalent small molecule inhibitors of USP30. 19 - Obaid Afzal, Ali Altharawi, Safar M. Alqahtani, Manal A. Alossaimi, Taibah Aldakhil, Abdulmalik S. A. Altamimi, Alhumaidi Alabbas, Mubarak A. Alamri:
Anticancer potential of novel benzothiazolyl piperidine-3-carboxamide derivatives as CDKs and VEGFR2 multi-target kinase inhibitors. 20 - Eman Shehab, Hamada Nayel, Mohamed Taha:
OPTUNA optimization for predicting chemical respiratory toxicity using ML models. 21 - Anaikutti Parthiban, Veeraragavan Sachithanandam, Perumal Lalitha, Priyanka Adhikari, Santhiyagu Prakash, Ramasamy Ramasubburayan, Deepika Dhillon, Jayaraman Muthukumaran, Nambali Valsalan Vinithkumar, Rengurajan Sridhar, Ramachandran Purvaja:
Decoding the multifunctional potential of ursolic acid: antioxidant, antiproliferative, molecular dynamics, and biodegradability evaluations of a mangrove-derived terpenoid. 22 - Balu Kamaraj, George Priya Doss C.:
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights. 23 - Pitchayakarn Takomthong, Pornthip Waiwut, Chantana Boonyarat:
Targeting multiple pathways with virtual screening to identify the multi-target agent for Alzheimer's disease treatment. 24 - Fahad M. Alshabrmi:
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach. 25 - Daniel K. Gehlhaar, Daniel J. Mermelstein:
Solvation and formal charge corrections to the Piecewise-Linear Potential. 26 - Mahir Azmal, Jibon Kumar Paul, Md. Naimul Haque Shohan, A. N. M. Shah Newaz Been Haque, Mohua Mrinmoy, Omar Faruk Talukder, Ajit Ghosh:
Evaluating computational and experimental approaches in early-stage Alzheimer's drug discovery: a systematic review. 27 - Na-Na Tan, Jia Lu, Zhuang-Hong Li, Shi-Ping Zhang, Huan Wang, Jing-Bo Hu, Tian Wang, Jian Xiao, Xiao-Ling Wang, Le Wang:
A systematic insight into glycycoumarin as potential IL-8/topo I inhibitor from natural products collected in Taibai mountain based on the combination of in silico and bioassay. 28 - Afzal Hussain, Md. Nayab Sulaimani, Shumayila Khan, Saleha Anwar, Mohammed F. Hawwal, Mohamed F. Alajmi, Dharmendra Kumar Yadav, Md. Imtaiyaz Hassan:
Structure-guided discovery of microtubule affinity-regulating kinase 4 inhibitory potential of Harmane: towards therapeutic targeting of Alzheimer's disease. 29 - Karishma Sen, Anita Sakarwal, Kamlesh Kumar, Heera Ram, Garima Singh, Vikas Kumar, Anil Panwar, Mukesh Kumar Yadav, Jing-Hua Wang:
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study. 30 - Priya Mishra, Swati Vipsita:
DTBA-net: Drug-Target Binding Affinity prediction using feature selection in hybrid CNN model. 31 - Adittya Pal:
Thermodynamic free energy map for the non-oxidative glycolysis pathways. 32 - Alya Mashaal, Basma M. Abou El-Nour, Fatma M. Ismail, Eman A. Elewa, Eman A. Elnoby, Eman B. Ebada, Ayaat G. Mohammed, Manar F. El-Sahmawy, Mariam M. Mansour, Nermeen N. Khames, Hend M. Ghorab, Safaa A. Osman, Alshimaa A. Elsaid, Maryam M. Abd-Alaziz, Asmaa S. Zayed, Asmaa A. Abo Elqasem:
Computer-aided molecular and biological-immune modeling of illicium verum bioactive compounds employing the Egyptian Nile snail Biomphalaria alexandrina as a paradigm. 33 - Mekala Prabhavathi, Bijaya Ketan Sahoo, Anna Tanuja Safala Bodapati, Bethala Samuel Raju:
An in-vitro and in-silico approaches in exploring the molecular contact of COVID-19 antiviral drug molnupiravir with human serum albumin: effect of binding on protein structure. 34 - Emadeldin M. Kamel, Ahmed A. Allam, Hassan A. Rudayni, Fahad M. Alshabrmi, Faris F. Aba Alkhayl, Al Mokhtar Lamsabhi:
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders. 35 - Pooja Dash, Pratyush Pragyandipta, Srinivas Kantevari, Pradeep Kumar Naik:
N-imidazopyridine derivatives of noscapine as potent tubulin-binding anticancer agents: chemical synthesis and cellular evaluation. 36 - Priya Kumari, Kumud Pandav, Anuradha Panwar, Shrikant Kukreti, Mala Nath, Ritu Barthwal, Surat Kumar:
Elucidating the binding mechanism of 1,4-bis[(3-Piperidino)propanamido]anthracen-9,10-dione (1,4-BPAQ) to human telomeric G-quadruplexes: a multi-technique approach including spectroscopic, calorimetric and molecular docking insights. 37 - Pinky Arora, Aditi Rana, Azmat Ali Khan, Amer M. Alanazi, Pankaj Wadhwa, Sonia Singla, Shubham Kumar, Rubal kalra:
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy. 38 - Vladimir Porokhin, Anne M. Brown, Soha Hassoun:
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones. 39 - Ioannis Liliopoulos, Georgios D. Varsamis, Theodora Karamanidou, Christos Papalitsas, Grigorios Koulouras, Vassilios Pantazopoulos, Thanos G. Stavropoulos, Ioannis G. Karafyllidis:
Quantum algorithm for protein-ligand docking sites identification in the interaction space. 40 - Muzaffar Kayumov, Jamoliddin I. Razzokov, Mukhriddin Makhkamov, Murodjon Radjabov, Nurkhodja Mukhamedov, Makhmudjon Khakimov, Akmal M. Asrorov, Okhunjon Khasanov, Ansor Yashinov, Mugrajitdin Tashmukhamedov, Ahmidin Wali, Abulimiti Yili, Sharafitdin Mirzaakhmedov:
3CLpro of SARS-CoV-2 as a new target for bufadienolides: in silico and in vitro study. 41 - Wali Ullah, Ghias Uddin, Abdur Rauf, Muhammad Umer Khan, Zuneera Akram, Chaudhry Ahmed Shabbir, Abdulhakeem S. Alamri, Walaa F. Alsanie, Marcello Iriti:
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation. 42 - Ahmad Syauqy Tafrihani, Naufa Hanif, I Made Bayu Kresna Yoga, Irmasari Irmasari, Taufik Muhammad Fakih, Dhania Novitasari, Poppy Anjelisa Zaitun Hasibuan, Denny Satria, Fathul Huda, Muchtaridi Muchtaridi, Adam Hermawan:
A computational study of cardiac glycosides from Vernonia amygdalina as PI3K inhibitors for targeting HER2 positive breast cancer. 43 - Hailong Bai, Yalong Cheng, Shunjiang Jia, Xiaorui Wang, Ruyi Jin, Hui Guo, Yuping Tang, Yuwei Wang:
Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products. 44 - Abdulwahab Alamri, Ahmed Alafnan, Weiam A. Hussein, Khaled Almansour, Alrafidi Rafidi Dhham, Amr S. Abouzied:
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective. 45 - Tu H. Tran, Tho H. Le, Thu-Ha T. Nguyen, Long B. Vong, Mai T. T. Nguyen, Nhan T. Nguyen, Phu Hao Dang:
New alkyl triphenylphosphonium dipterocarpol derivatives with cytotoxicity against the MCF-7 breast cancer cell line. 46 - Sonia Yahiaoui, Sabiha Khamtache-Abderrahim, Djamel Edine Kati, Nadir Bettache, Mostapha Bachir-bey:
Anti-inflammatory potential of isoquinoline alkaloids from Fumaria officinalis: in vitro, in vivo, and in silico evaluation. 47 - Sadettin Y. Ugurlu:
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches. 48 - Lokesh Ravi, Pratishtha Jain, Ajith Kumar K, Jeevan Kumar M, Mukti Panda, Harshitha S, Mohammed Abdul Kareem, K. Sivani Yelchuri Sai, Ayman Fathima, V. Jensha, Adarsh Anurag Rai, Hida Amal Faizal, Shrivats S. R, Ankitha Ajith, Derick Yesudas, Vaarruni S, Varshini S, Raksha Shetty, Aditi Jha, Gundlapalli Saradha Janaki, Varsha Hannah George, Stalin Nithaniyal, Mookkandi Palsamy Kesavan, Sajith Ahamed A, Sankara Narayanan A:
"Heptadecanol" a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation. 49 - Pritimoni Das, Manas Das:
Therapeutic potency of a developed optimized polyherbal formulation in ameliorating obesity induced inflammation and oxidative stress in Swiss albino mice by targeting PPARγ, insulin receptor and AMPK signalling pathway. 50 - Ashis Nandy, Kiran Boppana, Samiron Phukan:
Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders. 51 - Georgios Iakovou, L. Palmer, A. Ganesan, Akio Kitao, Stephen D. Laycock, Steven Hayward:
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study. 52 - Ya Zhou, Ben-Rong Mu, Xing-Yi Chen, Li Liu, Qing-Lin Wu, Mei-Hong Lu, Feng-Ling Qiao:
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer's disease. 53 - Yongrui Cui, Dongjing Shan, Qiheng Lu, Beijia Zou, Huali Zhang, Jin Li, Jiashun Mao:
Comparison study of dominant molecular sequence representation based on diffusion model. 54 - Han Liu, Roufen Chen, Dandan Yuan, Yidan Xing, Xueyan Ding, Xingye Wu, Yali Gao, Junjie Ma:
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors. 55 - Wali Ullah, Ghias Uddin, Abdur Rauf, Muhammad Umer Khan, Zuneera Akram, Chaudhry Ahmed Shabbir, Abdulhakeem S. Alamri, Walaa F. Alsanie, Marcello Iriti:
Anti-inflammatory potential of Grewialin from Grewia optiva: insights from molecular docking, ADMET, DFT, and in-vitro studies. 56 - Chen Fei Low, Norazli Ghadin, Muhamad Arif Mohamad Jamali:
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins. 57 - Sanjay Soni, Khushbu Patil, Sharad Gavale, Soyeb Pathan, Rasana Yadav, Prashant Revan Murumkar, Rahul Kadu:
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation. 58 - Olajide B. Omoyeni, Kolade Olatubosun Faloye, Rajesh B. Patil, Emmanuel G. Fakola, Sulaimon Olatunji, Ayobami J. Olusola, Felix Olusegun Gboyero, Ahmad J. Obaidullah, Jawaher M. Alotaibi:
Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives. 59 - Xiao Wang, Ziwei Liu, Daolai Zhang, Yulong Wu, Yongfeng Li, Xiaowei Chen:
Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7. 60 - Mariya L. Ivanova, Nicola Russo, Konstantin Nikolic:
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn. 61 - Manasa Gangadhar Shetty, Bipasa Dey, Padmini Pai, Babitha Kampa Sundara, Kapaettu Satyamoorthy, Srinivas Oruganti, Usha Yogendra Nayak, T. Ashwini:
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy. 62 - Yu Yunxiang, Zhang Zhou, Guo Hai, Ren Xinlu, Zhang Yuting, Meng Jianna, Zhou Yi, Han Jian, Tian Jinhui, Yan Wenjin, Huang Jinqi:
Ai-driven de novo design of customizable membrane permeable cyclic peptides. 63 - Ismahene Ben Khemis, Bouzid Gassoumi, Fatma Aouaini, Salah Knani, Besma Graba, Ghadeer Mohsen Albadrani, Abdelmottaleb Ben Lamine:
Advanced investigation of the adsorption process of geosmin molecules on polar bear and camel olfactory receptors: statistical physics treatment, in-depth DFT-modeling, and docking analysis. 64 - Shankar G. Alegaon, Shriram D. Ranade, Shankar Gharge, Rohini S. Kavalapure, Venkatasubramanian Ulaganathan:
Computational and experimental repositioning of quinoline analogues as KSP inhibitors: insights from free energy landscape and PCA analysis. 65 - Tadeusz W. Inglot:
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets. 66 - Katarzyna Madra-Gackowska, Szymon Baumgart, Mateusz Jedrzejewski, Renata Studzinska, Lukasz Szeleszczuk, Marcin Gackowski:
Computational QSAR study of novel 2-aminothiazol-4(5H)-one derivatives as 11β-HSD1 inhibitors. 67 - Lin Wei, Yihe Fang, Peng Chen, Zigong Wei:
Application of directed message-passing neural network to predict human oral bioavailability of pharmaceuticals. 68 - Xiuzhi Jia, Qinglian Han, Xiaoqun Ma, Zhongwen Sun:
Structure-based drug design of small molecule AKT1 inhibitors to treat glioma. 69 - J. Sneha, V. Abinaya, R. Akash, R. M. Hariharan, K. Janani Sivasankar, D. John Thiruvadigal:
Exploring the structural and electronic properties of boron nitride nanotube (BNNT) as nanocarrier for drug delivery applications: DFT approach. 70
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