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ORCIDComputational Biology and Chemistry, Volume 118
Volume 118, 2025
- Jehad Zuhair Tayyeb, Imren Bayil, Taha Alqahtani, Gabriel Vinícius Rolim Silva, Guilherme Bastos Alves
, Al-Anood M. Al-Dies, Abdelkrim Guendouzi, Jonas Ivan Nobre Oliveira, Magdi E. A. Zaki:
Identification of Therapeutic Compounds Targeting Phosphatidylinositol 3-Kinase (PI3K) Through Molecular Docking, Dynamics Simulation, and DFT Calculations. 108433 - Watshara Shoombuatong, Saeed Ahmed, S. M. Hasan Mahmud, Nalini Schaduangrat:
A comprehensive review and evaluation of machine learning-based approaches for identifying tumor T cell antigens. 108440 - Gayathri Krishnamurthy Ganga:
Accelerating drug discovery targeting dihydroorotate dehydrogenase using machine learning and generative AI approaches. 108443 - Orkid Coskuner-Weber, Semih Alpsoy, Ozgur Yolcu, Egehan Teber, Ario de Marco, Spase Shumka:
Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing. 108444 - Elkin Sanabria-Chanaga, Edwin L. Bonilla-Rozo:
Insights from computational studies about structural determinants of steroidal inhibitors in 5-alpha-reductase type II. 108446 - Sri Mounika Bellapukonda, Siva Singothu, Anuradha Singampalli, Rani Bandela, Pardeep Kumar, Venkata Madhavi Yaddanapudi, Vasundhra Bhandari, Srinivas Nanduri, Mohamed Enneiymy, Mohamed Fahad AlAjmi, Ali Oubella:
Exploring spirocyclic isoquinoline-piperidine compounds in tuberculosis therapy: ADMET profiling, docking, DFT, MD simulations, and MMGBSA analysis. 108447 - Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leyi Wei, Quan Zou, Feifei Cui:
PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. 108448 - Xudong Lü, Chenyu Wang, Mengjia Tang, Jing Li, Zhiyong Xia, Shuai Fan, Yuanyuan Jin, Zhaoyong Yang:
Pinpointing potent hits for cancer immunotherapy targeting the TIGIT/PVR pathway using the XGBoost model, centroid-based virtual screening, and MD simulation. 108450 - Santhiya Panchalingam, Govindaraju Kasivelu:
Harnessing marine bioactive compounds: In silico insights into therapeutics for rheumatoid arthritis and major depressive disorder. 108452 - Anmol Kulshrestha, Pratima Gupta:
Multi-computational screening identifies homovanillic acid as a potential SAP5 inhibitor against Candida albicans biofilms. 108453 - Sanjay Gopi, S. Madesh, Karthikeyan Ramamurthy, Mikhlid H. Almutairi, Bader O. Almutairi, S. Karthick Raja Namasivayam, Jesu Arockiaraj:
Black seed (Nigella sativa) extract enhances early and late apoptosis through activation of caspase-3 mediated regulatory pathway in LC540 cells: A network pharmacological and molecular docking approach. 108455 - Smritilekha Das, Padmanaban Kuppan:
Incremental learning for acute lymphoblastic leukemia classification based on hybrid deep learning using blood smear image. 108456 - Jianjian Zhong, Xiaohua Fan:
Chinese herbal extract Astragalus radix potentiates human ovarian cancer cell cytotoxicity by aggravated ROS production and apoptosis. 108457 - Long Cheng, Weizhong Lu, Yiyi Xia, Yiming Lu, Jiyun Shen, Zhiqiang Hui, Yixin Xu, Hongjie Wu, Jing Chen, Qiming Fu, You Lu:
ProAttUnet: Advancing protein secondary structure prediction with deep learning via U-Net dual-pathway feature fusion and ESM2 pretrained protein language model. 108429 - Chang Li, Jia Mi, Han Wang, Zhikang Liu, Jingyang Gao, Jing Wan:
MGMA-DTI: Drug target interaction prediction using multi-order gated convolution and multi-attention fusion. 108449 - Pradeep Kumar Yadalam, Swarnambiga Ayyachamy, Francisco T. Barbosa, Prabhu Manickam Natarajan:
Kolmogorov-Arnold networks for predicting drug-gene associations of HDAC1 inhibitors in periodontitis. 108451 - Gideon Ampoma Gyebi, Saheed Sabiu:
Structure-based profiling of putative therapeutics against monkeypox virus VP39 using pharmacophore modelling and molecular dynamics simulation studies. 108458 - Ramanjaneyulu Golla, Sneha Jaiswal, Anaswara Jayan, Srinivasulu Cheemanapalli:
Transcriptomic analysis of human castration-resistant prostate cancer: Insights into novel therapeutic strategies. 108459 - Om Prakash Sharma:
PathwayMind: An innovative tool and database for pathway perturbation analysis, uncovering critical pathways for drugs and target protein sets. 108466 - Mohamed J. Saadh, Hanan Hassan Ahmed, Radhwan Abdul Kareem, Muktesh Chandra, Lokesh Verma, G. V. Siva Prasad, Anurag Mishra, Waam Mohammed Taher, Mariem Alwan, Mahmood Jasem Jawad, Atheer Khdyair Hamad:
The drug discovery candidate for targeting PARP1 with Onosma. Dichroantha compounds in triple-negative breast cancer: A virtual screening and molecular dynamic simulation. 108471 - Uma E., Mala T.:
DICCA-DTA: Diffusion and Contextualized Capsule Attention guided Factorized Cross-Pooling for Drug-Target Affinity prediction. 108472 - Rufeng Lei, Jian Jia, Lulu Qin:
im7G-DCT: A two-branch strategy model based on improved DenseNet and transformer for m7G site prediction. 108473 - Mohamed Abd Elaziz, Diego Oliva, Alaa A. El-Bary, Ahmad O. Aseeri, Rehab Ali Ibrahim:
Dynamic comprehensive learning-based dung beetle optimizer using triangular mutation for polyps image segmentation. 108474 - Yun Fan, Xiaolong Wang, Yun Ling, Qiuyi Wang, Xibin Zhou, Kai Li, Chunxiang Zhou:
Identification and validation of biomarkers in Alzheimer's disease based on machine learning algorithms and single-cell sequencing analysis. 108475 - Samet Kocabay, Erdi Acar, Samet Memis, Irmak Içen Taskin, Meryem Rüveyda Sever, Ramazan Sener:
Prediction of newly synthesized heparin mimic's effects as heparanase inhibitor in cancer treatments via variational quantum neural networks. 108476 - Soumaya Zaghbani, Lukas Faber, Ana J. Garcia-Saez:
Convolutional Neural Network approach to classify mitochondrial morphologies. 108477 - Nachiket Joshi, Rajasekhar Reddy Alavala:
Identification of novel ligands against GSK-3β: Molecular docking, ADMET filtering, MD simulations, MM-GBSA studies, and DFT analysis. 108478 - Ying Wang, Jiaxin Lin, Bo Liang:
Enhancing lncRNA-disease associations predictions by optimizing similarity on multiple heterogeneous networks. 108479 - Seok-Jin Kang, Hongchul Shin:
Amino acid sequence-based IDR classification using ensemble machine learning and quantum neural networks. 108480 - Priyadharshini Annadurai, Arnold Emerson Isaac:
Prediction of key pathways in hepatocellular carcinoma (HCC): A machine learning approach using a sample pathway information matrix. 108481 - Farong Liu, Sheng Ren, Jie Li, Haoyang Lv, Fenghui Jiang, Bin Yu:
SGTB: A graph representation learning model combining transformer and BERT for optimizing gene expression analysis in spatial transcriptomics data. 108482 - Junnan Li, Wei Zhang, Qi Dai:
scDGG: Dynamic gene graphs for enhancing clustering analysis of single-cell RNA sequencing data via spatiotemporal representations. 108483 - Yongxian Fan, Chen Wang, Guicong Sun:
iEnhancer-DS: Attention-based improved densenet for identifying enhancers and their strength. 108484 - Dangguo Shao, Yuyang Zou, Lei Ma, Sanli Yi:
Multiscale and global-local U-Net for protein-protein interaction site prediction. 108485 - Halil Senol, Namik Kilinç, Furkan Çakir, Gürgün Albay, Feyzi Sinan Tokali:
Synthesis and evaluation of aldose reductase inhibition of new thiazolidine-quinazoline hybrids through in vitro and in silico approaches. 108486 - Ganesh Sanjay Kakde, Tikam Chand Dakal, Pawan Kumar Maurya:
Understanding the IDH1 missense SNPs on expression of genes involved in Glioblastoma multiforme. 108487 - Khushboo, Manisha, Sanchita Aggarwal, Subhash, Neera Raghav, Heena Dahiya, Nitika Mor:
A virtual screening of Withaniasomnifera compounds using ADMET predictions, molecular docking, MD simulation and DFT calculations: Withasomniferol C an effective drug and potent inhibitor of anti-inflammatory targets. 108488 - Yahya Güzel, Sevcan Karakaya, Lichang Wang, Burçin Türkmenoglu, Dilek Seyma Kizilcan:
3D-QSAR modeling with selection of local reactive descriptors (LRD) and molecular docking studies on diarylpyrazole-benzenesulfonamide derivatives. 108489 - Fatma S. Ahmed, Saleh K. H. Aly, Mohamed A. M. El-Tabakh, Xiangrong Liu:
NABP-LSTM-Att: Nanobody-Antigen binding prediction using bidirectional LSTM and soft attention mechanism. 108490 - Kaibiao Lin, Fengxin Huang, Shuangta Zhuo, Qiqi Zhou, Dawei Pan, Shenbao Yu, Fan Yang:
Asymmetric drug interaction prediction via multi-scale fusion of directed topological relationships and drug features. 108491 - Balaji Wamanrao Matore, Anjali Murmu, Purusottam Banjare, Naveen Kumar Vishvakarma, Partha Pratim Roy, Jagadish Singh:
Discovery of newer 1,3,4-Oxadiazole clubbed Isoindoline-1,3-dione derivatives as potential anticancer agents: Design, machine learning, synthesis, molecular docking, ADMET, DFT and MD simulation. 108492 - Veda Naga Priya Vangala, Vladimir N. Uversky:
Intrinsic disorder in protein interaction networks linking cancer with metabolic diseases. 108493 - Karthika Alagesan, Hemavathy Nagarajan, Amala Mathimaran, Umashankar Vetrivel, Veerapandiyan Malaisamy, Chun-Jung Chen, Jeyaraman Jeyakanthan:
A promising strategy to disrupt Plasmodium falciparum metabolic resilience by targeting G6PD: Virtual screening for potential inhibitors against malaria. 108495 - Hamid Ullah, Aftab Alam, Ahmed A. Elhenawy, Imtiaz Ahmad, Abdul Latif, Mumtaz Ali, Manzoor Ahmad:
Exploring the anti-diabetic potential of bis-Schiff base derivatives of benzimidazole: In-Vitro α-amylase, α-glucosidase inhibition, molecular docking, ADMET and DFT studies. 108497 - Ezaddine Irrou, Younesse Ait Elmachkouri, Olivier Blaqcue, Ali Oubella, Md Tabish Rehman, Mohamed Fahad AlAjmi, Nada Kheira Sebbar, Mohamed Labd Taha:
Synthesis, X-ray diffraction, and computational studies of acyclovir and HBG analogs derived from Triazolyl-1,4-benzothiazine and their oxidized forms for breast cancer and SARS-CoV-2. 108498 - Ruqqaya Javid, Shahnawaz Ahmad Dar, Suma Mohan, Zahoor Ahmad Baba, Faheem Jeelani Wani, Munazah Yaqoob, P. M. Osman Javid, Shahid Ahmad Padder, Shabir Ahmad Ganai:
Comparative anti-oxidant and anti-inflammatory study of diverse honey types of Kashmir valley through In Vitro, analytical chemistry and computational approach. 108499 - Mustafa Alhaji Isa, Abidemi Paul Kappo:
Machine learning-driven discovery of antimicrobial peptides targeting the GAPDH-TPI protein-protein interaction in Schistosoma mansoni for novel antischistosomal therapeutics. 108501 - Shilu Kang, Hua Huo, Aokun Mei, Jiaxin Xu:
UB-Former: A fine-grained classification method for images of insects using biomorphic features. 108496 - Tathagat Banerjee:
Towards automated and reliable lung cancer detection in histopathological images using DY-FSPAN: A feature-summarized pyramidal attention network for explainable AI. 108500 - Muath Suliman, Aqsa Laraib, Shamsa Bibi, Shimmaa Mansour Moustafa Mohamed, Mohammad Y. Alshahrani, Shabbir Muhammad:
The exploring AI-generated pyrazalone derivatives as antifungal agents: Bringing together molecular docking and quantum chemical approaches. 108502 - Nabeela Kausar:
Machine learning and explainable artificial intelligence reveals the MicroRNAs associated with survival of head and neck squamous cell carcinoma patients. 108503 - Komal Kumari, Gyan Prakash Rai, Srishti Shriya, Nooruddin Khan, Mohammad Shamsul Ola, Asheesh Shanker, Rizwanul Haque:
Coevolutionary dynamics of 53BP1 and its impact on TP53 interaction for DNA damage repair. 108508
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