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ORCIDComputational Biology and Chemistry, Volume 119
Volume 119, 2025
- Xin Ma
, Dong Si:
Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps. 108494 - Rezvan Rahimi, Mohammad Solimannejad, Mohammad Hossein Abnosi:
In silico study of salicylic acid derivatives as inhibitors of Ebola proteins through molecular docking. 108504 - Ali Rejwan Kabir, Soumita Podder:
An integrated bioinformatics and machine learning-based approach to depict key immunological players associated with candidemia during immunodeficiency. 108505 - Yuankai Lv, Xiaoping Cai, Hao Zheng, Hong Dai:
Identification of different lung adenocarcinoma subtypes in combination with antidiuretic hormone-related genes and creation of an associated index to predict prognosis and guide immunotherapy. 108506 - Mei-zhen Liang, Xian-feng Huang, Jun-chang Zhu, Jing-xia Bao, Cheng-Liang Chen, Xiao-wu Wang, Yun-wei Lou, Ya-ting Pan, Yin-wei Dai:
A machine learning-based glycolysis and fatty acid metabolism-related prognostic signature is constructed and identified ACSL5 as a novel marker inhibiting the proliferation of breast cancer. 108507 - Zhuokun Tan, Longfei Luo, Jingjing Yang, Xiang Zhang, Zimin Yu, Ming Huang, Shunfang Wang:
EFM2BF: Extraction and fusion of multi-network multi-scale bio-topological features for gene prediction in brain diseases. 108509 - Pengyu Yang, Peng Feng, Guopeng Tian, Guomin Zhao, Guoqiang Yuan, Yawen Pan:
Integrative machine learning and bioinformatics analysis unveil key genes for precise glioma classification and prognosis evaluation. 108510 - Hamed Ka, Jafar Razmara, Sepideh Parvizpour, Morteza Hadizadeh:
Alzheimer's diagnosis by an efficient pipelined gene selection model based on statistical and biological data analysis. 108511 - Nishasri Sukumaran, C. S. Sureka, P. Gurusaravanan, V. Thirunavukkarasu, R. Alagupandi, T. Priyadharshini:
Investigations on bioactive compounds of Punica granatum and Beta vulgaris for breast cancer treatment: Network pharmacology predictions, molecular docking, and in-vitro experimental verification of radiation-sensitizing effects. 108512 - Sachendra Kumar, Tamasa De, Janavi Subramani, Annapoorni Rangarajan, Debnath Pal:
Combined analysis of somatic mutations and gene expression reveals nuclear speckles-associated enhanced stemness in gingivobuccal carcinoma under DNA damage response. 108513 - Elaheh Hosseinzadeh, Loghman Firoozpour, Massoud Amanlou:
Identification of natural inhibitors against CDK6 target using pharmacophore-based screening, molecular docking, molecular dynamic simulations, and quantitative electrostatic potential analysis maps: A comprehensive study. 108514 - Lokman Ali Ahmed, Babita Deka, Hiyashree Sharmah, Pooja Patowary, Bhargab Jyoti Sahariah, Apurba Talukdar:
Design and synthesis of novel xanthone-thiazole hybrid derivatives as potent anti-inflammatory agent. 108523 - Shefin B, Pinkie Cherian, Aji Abraham, Srinivasan Prabhu, Singamoorthy Amalraj, Jeyalatchagan Sureshkumar, Sharifa Jameel Hossain, Quratulain Zafar:
Unravelling the untapped antifungal potential of polyphenolic compounds by targeting aspartate-beta-semialdehyde dehydrogenase: Insights from multifaceted drug design approaches. 108524 - Arunmozhi Bharathi Achudhan, Lilly M. Saleena:
In silico analysis to identify novel amidase enzymes from unclassified bacteria present in coal metagenome. 108525 - Sanjib Kumar Mohanty, Achyutananda Samal, Elora Barik, Srikanta Jena, Yashaswi Nayak:
Integrated in silico and GC-MS analysis of Momordica charantia Linn. phytocomponents against DiNP phthalate and B[a]P toxicity: A focus on amyloid beta protein and acetylcholinesterase in neurodegenerative disease. 108526 - Nizakat Ali, Urooj Qureshi, Asaad Khalid, Zaheer-ul-Haq:
Integrative strategies in drug discovery: Harnessing genomics, deep learning, and computer-aided drug design. 108530 - Ali B. M. Ali, Ehab Yassen Theab, Muyassar Norberdiyeva, Prakash Kanjariya, Suhas Ballal, Apurav Gautam, Subhashree Ray, Aashna Sinha, Mustafa Shakir, Ahmed Naglah, Khursheed Muzammil:
A computational investigation of monolayer HB: Effective NH3 gas sensor with highly sensor response. 108531 - Fazal Hadi, Fatima Noor, Haseeba Sardar, Hany W. Darwish, Usman Ali Ashfaq, Ashraf Ali Khan, Maria Daglia, Haroon Khan:
Integrating in vitro, network pharmacology, and molecular docking approaches to uncover the antidiabetic potential of Tylophora hirsuta. 108533 - Selinay Cetin, Emre Sefer:
The significance of chromosome conformation capture in 3D genome architecture comprehension. 108534 - Imran Zafar, Ahsanullah Unar, Najeeb Ullah Khan, Adil Abalkhail, Adil Jamal:
Molecular biology in the exabyte era: Taming the data deluge for biological revelation and clinical transformation. 108535 - Tamizhini Loganathan, Karthick Vasudevan, John Fletcher, Priya Abraham, Rajesh kannangai, George Priya Doss C.:
Mutational dynamics and phylogenetic insights into monkeypox virus clade I evolution. 108536 - Istiaq Ahmed, Stephen Woodward, Gareth J. Norton:
Genome-wide association mapping of bakanae disease resistance in rice. 108538 - Fan Huang, Hongjie Gao, Yanping Wang, Ding Li, Zhiyi Lu, Luqiu Chen, Fengyin Sun:
Expression of the immune gene related to energy metabolism (NDRG1) in Wilms' tumor and its correlation with prognosis. 108540 - Vishnupriya Chandrasekaran, Gopinath Samykannu, Jeykumar Natarajan, Kavitha Rangasamy:
Revelation of Brevi-inflammin, a novel anti-inflammatory metabolite from Brevibacterium casei VRK 1, as a potent COX-2 inhibitor. 108541 - Gauri Shankar, Yusuf Akhter:
Identification of IrtAB inhibitors as novel therapeutic agents against drug-resistant Mycobacterium tuberculosis. 108542 - Amgad M. Rabie, Meriem Khedraoui, Samir Chtita:
Targeting conserved regions of the SARS-CoV-2 polymerase (RdRp) with kinase inhibitors as an effective new tactic for discovering dual-action "antiviral-antiinflammatory" drugs against COVID-19. 108454 - Waseem, Zeshan Faiz, Shazia Habib, Faiza, Nisreen Innab:
Optimizing tomato plant and insect disease control using a fractional model and deep neural networks. 108515 - Latefa Oulladji, Mouna Saadallah, Zakaria Guellil, Houda Abbad, Houda Bekhti:
AI-Driven molecule generation and bioactivity prediction: A multi-model approach combining VAE, graph and language-based neural networks. 108532 - Shoaib Khan, Tayyiaba Iqbal, Muhammad Bilal Khan, Rafaqat Hussain, Mohammad Shahidul Islam, Eman Alzahrani:
Novel oxazole based oxadiazole conjugates: Synthesis, DFT study and in silico confirmation as potent anti-diabetic agents. 108537 - Anamika Das, Monalisa Mandal:
Integrating machine learning and statistical methods for prediction and feature-based network characterization of stress response protein. 108539 - Alen Cebzan, Dusan Ruzic, Nemanja Djokovic, Branislav Stankovic, Katarina Nikolic:
A computational framework for the design and development of ERK2 and multi-target ERK2/HDAC inhibitors. 108543 - Merin Manuel, Parthiban A.:
A graph-theoretical approach to characterizing anaesthetic agents using topological indices and QSPR models. 108544 - Trisha Patra, Sanjit Dey, Soma Barman Mandal:
Cytomorphic electronic system design of apoptosis pathway with extrinsic and intrinsic perturbations. 108545 - Tamil Barathi Palanisamy, Mohanapriya Arumugam:
Transcriptomic profiling and biomarker discovery in pre-eclampsia: An integrated approach leveraging WGCNA and LASSO with ROC validation. 108546 - Muhammad Farman, Aamir Shehzad, Faisal Sultan, Kottakkaran Sooppy Nisar, Mustafa Bayram, Aceng Sambas:
A kinetic model with analysis for the oxidation of sugars by permanganate in simple aqueous media with sustainable fractional approach. 108547 - Phu Pham:
An enhancement of multi-scope topological graph pooling and representation learning with attention for molecular graph classification. 108548 - Innasi Lineta P., J. Jerusalin Carol:
SECOA: Serial Exponential-Crayfish Optimization Algorithm with ResNet features for medical image registration. 108549 - G. Indu Salini, I. Sowmy, T. K. Sreeja:
FrAdadelta-CSA: Fractional Adadelta Chameleon Swarm Algorithm-based feature selection with SpikeGoogle-DenseNet for epileptic seizure detection. 108550 - Malathy Manickavasagam, Vaddadi Vasudha Rani, Uttam Kumar Giri, Balajee Maram:
Skin cancer detection using harmonic brown bear optimization enabled transfer learning. 108551 - Liling Zhao, Li Zhao, Haiyan Li, Zanxia Cao:
Effects of toxin peptides PepA1 and PepA2 on human red blood cell membrane model: A molecular dynamics study. 108552 - Shengpeng Wang, Yongzhu Zhao, Jiawei Li, Lifu Zhang, Fei Yan, Cuihong Wang, Liying Shi, Xinge Zhang, Meiling Zhang:
Computational discovery of RSV Pre-F inhibitors via reinforcement learning-driven ab initio design from natural fragment libraries. 108553 - Kai Zhang, Yunmei Zhu, Wei Zhang, Yanghan Sun, Ziheng Zhang, Yueyang Wang, Yixian Tan, Linyu Yu, Sirui Chen, Shiyong Ma, Kongkai Zhu, Bowen Ke, Jiaxue Wu, Zufeng Guo, Ling Zhang, Yongjun Dang, Junchi Hu:
LigDockTailor: Ligand-specific docking tool matching using multidimensional descriptors. 108554 - Jamshaid Ul Rahman, Hasnain Ali, Areen Rassol:
A comprehensive analysis of optimizers in message passing neural networks for molecular property prediction task. 108556 - Geetashree Gyanadarshinee Sahoo, Ananya Nayak, Ayushman Gadnayak, Biswabhusan Dash, Sudipta Jena, Asit Ray, Pratap Chandra Panda, Sanghamitra Nayak, Ambika Sahoo:
Computer-aided screening of phytoconstituents from Plumeria species targeting xanthine oxidase inhibition: a combination of pharmacokinetics, molecular docking and molecular dynamics approaches. 108557 - W. Eltayeb Ahmed, Muhammad Farhan Hanif, Mazhar Hussain, Muhammad Kamran Siddiqui:
A comprehensive study on topological indices and entropy measures for terbium niobate using logarithmic regression models. 108558 - Zeqiang Xian, Caihui Liu:
A systematic framework enhancing molecular screening efficiency in drug discovery via scaffold-driven fuzzy similarity and adaptive spectral clustering. 108559 - Yosui Nojima, Kenji Mizuguchi:
Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning. 108560 - Herlin L. T., A. Lenin Fred:
Fertilizer prediction using serial exponential newton meta-heuristic algorithm-based convolutional neural network in IoT-based WSNs. 108561 - Sharma Manjunath Arun, Neerkaje Subrayabhat Devaki:
Decoding the role of novel long noncoding RNAs lnc-SLC6A12-1:3 and lnc-SLC6A12-7:5 in regulating the expression of GAD1 and SLC6A12 in cholangiocarcinoma. 108562 - Xiao Rao, Yiling Zhou, Jianbo Xue, Zhiyou Zhou:
Identification of DNA damage repair-related diagnostic markers for idiopathic pulmonary fibrosis via WGCNA. 108563 - Poornima Baskar Vimala, Leela kagithakara Vajravelu, Rahul Harikumar Lathakumari, Vishnu Priya Panneerselvam, Dakshina M. Nair, Jayaprakash Thulukkanam:
Targeting cadherins with colicins: Molecular docking and dynamics reveal disruptive potential in cancer metastasis. 108564 - Sher Wali Khan, Haroon Rashid, Saira Nayab, Husna, Momin Khan, Lubna Rasheed:
Synthesis, In Vitro, and In Silico studies of imide derivatives of phthalic anhydride as potential antimicrobial agents. 108565 - Wei Zhang, Yue-Na Wang, Hui Sun:
Lactate dehydrogenase B A Hypoxia and lactylation relative-gene as potential biomarkers for alcoholic liver disease: Integration of single-cell, bulk RNA-sequencing and experimental validation. 108566 - Subodh Soni, Priyanka, Pooja Chugh, Nisha Ghanghas, Manjeet Chahar, Sanjay Kumar, Manish Kumar Gupta, Hari Mohan:
Unravelling Pasteurella multocida Toxin (PMT): Structural insights, antibiotic assessment, and identification of potential inhibitors. 108567 - Devvrat Pandey, Shivam Kumar, Dipanka Sarmah, Samrat Chatterjee:
TCGAimmunosurv: An R package to identify genes associated with patient survival and immune cell state transitions using TCGA and single-cell RNA-seq data. 108568 - Singamoorthy Amalraj, Kalaimathi Karunanithi, Srinivasan Prabhu, Kaliyamoorthy Dass, Fadia Awadalkreem, Shine Kadaikunnan, Muthu Thiruvengadam:
Chemical constituents of vegetables and fruits as potential inhibitors of lipoprotein-associated phospholipase A2: An in-silico approach toward mitigating the complications of Alzheimer's disease and atherosclerosis. 108569 - Norma Flores-Holguín, Juan Frau, Daniel Glossman-Mitnik:
Exploring the reactivity landscape of bioactive peptides using conceptual DFT and molecular modeling tools. 108571 - Sharif Karim Sayyed, Marzuqa Quraishi, Satish Kumar Rajasekharan, Tareeka Sonawane, Vinothkannan Ravichandran:
Zinc C293 as a novel scaffold with dual activity against HIV-1 integrase and reverse transcriptase. 108573 - Vidya C. A., V. Baby Shalini:
DeepELR: Deep learning-based energy and link stability aware routing in IoT for heart disease classification. 108574 - Pijush Kanti Khanra, Thirukumaran Kandasamy, Siddhartha Sankar Ghosh:
Targeting the RARα-Gankyrin-PI3K axis with retinoid analogs to modulate autophagy in breast cancer cells: Computational insights and experimental validation. 108575 - Mahdie Eghdami, Mahmoud Naghibzadeh, Hamid Noori:
Accelerating long-read overlap detection for genome assembly with a two-hash table strategy. 108576 - Fengyue Zhang, Ruiqi Liu, Lichuan Wu:
GC-PGE: A novel deep learning model for tumor drug resistance prediction and core resistance gene extraction based on graph and signaling pathways. 108578 - Jun Su, Wenlong Sun, Bogdan Adamyk:
DSMT-Net: Dual-student mean teacher network with pixel-level pseudo-label optimization for semi-supervised medical image segmentation. 108579 - Younesse Ait Elmachkouri, R. Rajesh, Ali Altharawi, Alfind Paul Frit A, Manal A. Alossaimi, Yassine Riadi, Taibah Aldakhil, Mohamed Labd Taha, Reda A. Haggam:
Synthesis, molecular structure, spectroscopic, electronic properties, molecular docking, and molecular dynamics studies on novel 1,2,3-triazole-thiosemicarbazone: A potent breast cancer drug. 108580 - Bo Wang, Peilong Wu, Xiaoxin Du, Chunyu Zhang, Shanshan Fu, Tang Sun, Xue Yang:
Enhancing microbe-disease association prediction via multi-view graph convolution and latent feature learning. 108581 - Pankaj Bhowmik, Mostofa Kamal Nasir:
Anemia diagnosis from clinical records leveraging tree-driven and XAI-enhanced machine learning. 108582 - Praveenkumar Kochuthakidiyel Suresh, Yogalakshmi Venkatachalapathy, George Priya Doss C., Sangeetha Geminiganesan, Sudha Ekambaram, Mohanapriya C. D:
Molecular insights into steroid resistance in childhood nephrotic syndrome: Gene expression and prognostic miRNA signatures. 108584 - Ali Zamani, Ali Khelef, Pinank Patel, Ganesan Ezhilarasan, Kolsoom Ansar, Siya Singla, Badri Narayan Sahu, Sanjeev Kumar Shah, Pasupuleti Sasikiran:
Computational insights into B12N12 nanocage as a promising carrier for mesalazine delivery: a DFT study. 108585 - Ayesha Khaliq, Fahad Ahmad, Habib Ur Rehman, Saad Awadh Alanazi, Hamza Haleem, Kashaf Junaid, Elisavet Andrikopoulou:
Revolutionizing medical imaging: A cutting-edge AI framework with vision transformers and perceiver IO for multi-disease diagnosis. 108586 - Lantian Zhang, Fuyan Hu, Qingjia Chi, Bifeng Chen:
The conditional mutual information-based single-sample network biomarker approach reveals the critical transition moments of disease progression. 108587 - Essy Harnelly, Haya Maghfira, Didik Huswo Utomo, Zulkarnain Zulkarnain, Vita Meylani:
Computational prediction of the patchouli plant (Pogostemon cablin Benth.) as an antiaging agent through activation of telomerase enzyme in the PI3K-Akt pathway. 108588 - Jianming Rong, Hengjian Zhong, Yiwei Meng, Qiqi Jin, Yijian Zhang, Chunman Zuo:
HLIP: A pan-cancer model for histological image analysis in clinical research using TCGA. 108589 - Md. Nazim Uddin, Jie Wang, Md. Habibur Rahman Bhuiyan, Md. Mamunur Rashid, Md. Zia Uddin Al Mamun, Ashikujaman Syed, Miah Roney:
Exploring the anti-cancer potential of daidzin in breast cancer: Integrated bioinformatics and computational insights on oncogene inhibition. 108590 - Farag M. A. Altalbawy, Shaker Al-Hasnaawei, Prakash Kanjariya, Asha Rajiv, Abhinav Kumar, Aditya Kashyap, Helen Merina Albert, Sumit Pokhriyal:
Computational study of the adsorption and biosensing of cytosine and guanine nucleobases by Cu, Ni, Ag and Au cluster modified InSe nanosheets: Applications to DNA sequencing. 108591 - Mostafa Alizade-Harakiyan, Amin Khodaei, Hamed Zamani, Hamed Jalili-Majdi, Asghar Mesbahi:
Predicting radiation-acute esophagitis via machine learning algorithms. 108592 - Laurent Soulère, Christophe O. Soulage:
Glycated human serum albumin: Computational studies of drug binding through molecular docking and binding affinity prediction. 108593 - Muhammad Aqib Javed, Muhammad Khuram Shahzad, Hafiz Syed Muhammad Bilal Ali:
A novel regularization approach for loss functions to reduce instance imbalance in biomedical image segmentation. 108555 - S. Zulaikha Beevi, Vanitha L, Shoba B, K. Prabhu Chandran:
GShC-Net: Hybrid deep learning with DCTLAP feature extraction for brain tumor detection. 108577 - Xin Zhao, Kang Li, Tao Zhang, Shuxin Cui, Yahui Cao, Xue Jia:
A Multiple Environmental Parameters and Molecular Fingerprints Contribution model for prediction of Gibbs free energy. 108583 - Modhi O. Alotaibi:
A systems approach to pigmentation control by ascorbic acid esterified with coconut oil-derived medium-chain fatty acids: Investigated via network pharmacology, molecular dynamics, elastic network and Markov state models. 108594 - Muhammad Hussain, Yu-Yen Ou, Quang-Thai Ho:
mCNN-GenEfflux: enhanced predicting Efflux protein and their super families by using generative proteins combined with multiple windows convolution neural networks. 108595 - Rohit Pritam Das, Arun Kumar Pradhan:
Unveiling key hub genes in E. coli biofilm formation: An in silico approach integrating differential gene expression, biosurfactant targeting, MD simulation and MM-PBSA free energy calculations. 108596 - Smita Satish Pawar, Mangesh D. Nikose:
Integrative review of intelligent nuchal translucency for genetic disorder. 108597 - Kun Li, Tianshuang Xia, Bin Peng, Liyong Lai, Weiqing Fan, Yiping Jiang, Jianyong Han, Ruiqing Zhu, Tao Jiang, Ti Yang, Xiaoqiang Yue, Denghai Zhang, Hailiang Xin:
Bioinformatics analysis combined with experiments to unveil common hub genes, pathways, and transcription factor regulatory networks in ulcerative colitis and osteoporosis. 108598 - Rashmita Kumari Mohapatra, Lochan Jolly, Sarada Prasad Dakua:
Advancing explainable AI in healthcare: Necessity, progress, and future directions. 108599 - Vinothini Santhakumar, Nahren Manuel Mascarenhas:
Molecular insights into ATP-mediated NBD dimerization in an ABC transporter. 108600 - Shoaib Khan, Tayyiaba Iqbal, Rafaqt Hussain, Faez Falah Alshehri, Zafer Saad Al Shehri, Sobhi M. Gomha, Magdi E. A. Zaki, Hamdy Kashtoh:
Computationally guided design and synthesis of pyrimidine-oxazole hybrids as novel antidiabetic agents: kinetic and molecular interaction studies. 108602 - Junhao Yu, Cong Hui, Jianhua Jia:
MJnet: A lightweight RNN-based model for microRNA target site prediction. 108603 - Ali Kadhim Wadday, Sukaina Tuama Ghafel, Suraa Reaad, Mustafa M. Kadhim:
Theoretical design of metal-porphin systems for selective interaction with trace geosmin. 108604 - Tara Chand, Pankaj Vaishanavaa, Ashwini Kumar Dubey, Gauri Misra:
Identification of hub genes as potential diagnostic biomarkers for cervical cancer: A bioinformatic approach. 108605 - V. Vanitha Jain, Madhu Anabala, Deepak Sharma, Rajiniraja Muniyan:
Machine learning driven identification of therapeutic phytochemicals targeting Hepatocellular carcinoma. 108608 - Karthikeyan Ramamurthy, Sanjay Gopi, S. Madesh, B. Aswinanand, Preeya Negi, Jubie Selvaraj, Mikhlid H. Almutairi, Bader O. Almutairi, S. Karthick Raja Namasivayam, Muthu Kumaradoss Kathiravan, Jesu Arockiaraj:
Regulation of oxytocin receptor by zinc coumarin derivatives: a mechanistic approach to alleviate anxiety and enhance folliculogenesis in letrozole-induced PCOS in zebrafish model. 108610 - Xingze Fang, Yun Zuo, Youxu Tan, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng:
PreAIS: Prediction of A-to-I editing sites based on DNN-CNN deep learning models. 108612 - Sekar Hamsa, Suhani Pathak, Reema Mishra, Aparajita Mohanty:
Harnessing transcriptome data of Viola inconspicua for discovery of novel cyclotides and AEP ligases. 108614
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