Biomolecules

Authors and titles for February 2025

[1] arXiv:2502.00508 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL Show Chinese title

Title: PyMOLfold：在PyMOL中进行交互式蛋白质和配体结构预测

Colby T. Ford, Samee Ullah, Dinler Amaral Antunes, Tarsis Gesteira Ferreira

Comments: GitHub Repository: https://github.com/colbyford/PyMolfold

Subjects: Biomolecules (q-bio.BM)

[2] arXiv:2502.00647 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: On an RNA-membrane protogenome Show Chinese title

Title: 关于RNA-膜原型基因组

Michael Yarus

Comments: 8.5 pages, 4 figures with 7 panels, 42 references, 5720 words all-inclusive. Revision of ms that was on hold

Subjects: Biomolecules (q-bio.BM) ; Populations and Evolution (q-bio.PE)

[3] arXiv:2502.02371 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking Show Chinese title

Title: RAPID-Net：用于无结合位点依赖的对接的准确口袋识别

Yaroslav Balytskyi, Inna Hubenko, Alina Balytska, Christopher V. Kelly

Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; Biological Physics (physics.bio-ph) ; Medical Physics (physics.med-ph)

[4] arXiv:2502.03606 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Artificial Intelligence Approaches for Anti-Addiction Drug Discovery Show Chinese title

Title: 抗成瘾药物发现的人工智能方法

Dong Chen, Jian Jiang, Zhe Su, Guo-Wei Wei

Subjects: Biomolecules (q-bio.BM)

[5] arXiv:2502.03851 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Frustration In Physiology And Molecular Medicine Show Chinese title

Title: 生理学与分子医学中的挫折感

R. Gonzalo Parra, Elizabeth A. Komives, Peter G. Wolynes, Diego U. Ferreiro

Subjects: Biomolecules (q-bio.BM) ; Soft Condensed Matter (cond-mat.soft) ; Biological Physics (physics.bio-ph) ; Quantitative Methods (q-bio.QM)

[6] arXiv:2502.06107 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review Show Chinese title

Title: 非编码RNA在HIV转录与潜伏中的作用评估：综述

Xiangshuai Liu

Comments: arXiv admin note: This version removed due to inaccurate authorship and excessive verbatim text overlap from external sources. Author metadata has been truncated

Subjects: Biomolecules (q-bio.BM)

[7] arXiv:2502.06881 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: A Comprehensive Review of Protein Language Models Show Chinese title

Title: 蛋白质语言模型的全面综述

Lei Wang, Xudong Li, Han Zhang, Jinyi Wang, Dingkang Jiang, Zhidong Xue, Yan Wang

Subjects: Biomolecules (q-bio.BM)

[8] arXiv:2502.06883 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: QuantumDNA: A Python Package for Analyzing Quantum Charge Dynamics in DNA and Exploring Its Biological Relevance Show Chinese title

Title: QuantumDNA：用于分析DNA中量子电荷动力学并探索其生物学相关性的Python包

Dennis Herb, Marco Trenti, Marilena Mantela, Constantinos Simserides, Joachim Ankerhold, Mirko Rossini

Comments: 16 pages, 10 figures, Appendix present

Subjects: Biomolecules (q-bio.BM) ; Biological Physics (physics.bio-ph) ; Computational Physics (physics.comp-ph) ; Quantum Physics (quant-ph)

[9] arXiv:2502.06891 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: ScaffoldGPT: A Scaffold-based GPT Model for Drug Optimization Show Chinese title

Title: ScaffoldGPT：基于骨架的药物优化GPT模型

Xuefeng Liu, Songhao Jiang, Ian Foster, Jinbo Xu, Rick Stevens

Subjects: Biomolecules (q-bio.BM) ; Computation and Language (cs.CL) ; Machine Learning (cs.LG)

[10] arXiv:2502.07671 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Steering Protein Family Design through Profile Bayesian Flow Show Chinese title

Title: 通过轮廓贝叶斯流设计蛋白质家族

Jingjing Gong, Yu Pei, Siyu Long, Yuxuan Song, Zhe Zhang, Wenhao Huang, Ziyao Cao, Shuyi Zhang, Hao Zhou, Wei-Ying Ma

Subjects: Biomolecules (q-bio.BM)

[11] arXiv:2502.08772 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Persistent Sheaf Laplacian Analysis of Protein Flexibility Show Chinese title

Title: 蛋白质柔韧性分析的持久层 Laplacian 方法

Nicole Hayes, Xiaoqi Wei, Hongsong Feng, Ekaterina Merkurjev, Guo-Wei Wei

Subjects: Biomolecules (q-bio.BM) ; Quantitative Methods (q-bio.QM)

[12] arXiv:2502.09372 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Inverse problems with experiment-guided AlphaFold Show Chinese title

Title: 以实验为导向的AlphaFold反问题

Advaith Maddipatla, Nadav Bojan Sellam, Meital Bojan, Sanketh Vedula, Paul Schanda, Ailie Marx, Alex M. Bronstein

Subjects: Biomolecules (q-bio.BM)

[13] arXiv:2502.09860 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Gradient GA: Gradient Genetic Algorithm for Drug Molecular Design Show Chinese title

Title: 梯度遗传算法：药物分子设计的梯度遗传算法

Chris Zhuang, Debadyuti Mukherjee, Yingzhou Lu, Tianfan Fu, Ruqi Zhang

Subjects: Biomolecules (q-bio.BM) ; Computational Engineering, Finance, and Science (cs.CE) ; Machine Learning (cs.LG) ; Machine Learning (stat.ML)

[14] arXiv:2502.09943 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Fluorescence Phasor Analysis: Basic Principles and Biophysical Applications Show Chinese title

Title: 荧光相位分析：基本原理与生物物理应用

Alvaro A. Recoulat Angelini, Leonel Malacrida, F. Luis Gonzalez Flecha

Subjects: Biomolecules (q-bio.BM)

[15] arXiv:2502.10173 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Agentic End-to-End De Novo Protein Design for Tailored Dynamics Using a Language Diffusion Model Show Chinese title

Title: 使用语言扩散模型的基于代理的端到端从头蛋白质设计以实现定制动力学

Bo Ni, Markus J. Buehler

Subjects: Biomolecules (q-bio.BM) ; Mesoscale and Nanoscale Physics (cond-mat.mes-hall) ; Materials Science (cond-mat.mtrl-sci) ; Machine Learning (cs.LG)

[16] arXiv:2502.11001 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: CL-MFAP: A Contrastive Learning-Based Multimodal Foundation Model for Molecular Property Prediction and Antibiotic Screening Show Chinese title

Title: 基于对比学习的多模态基础模型 CL-MFAP：用于分子性质预测和抗生素筛选

Gen Zhou, Sugitha Janarthanan, Yutong Lu, Pingzhao Hu

Comments: Gen Zhou and Sugitha Janarthanan contributed equally; Accepted at ICLR 2025

Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; Quantitative Methods (q-bio.QM)

[17] arXiv:2502.11326 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Deep Learning of Proteins with Local and Global Regions of Disorder Show Chinese title

Title: 蛋白质的深度学习：局部和全局无序区域

Oufan Zhang, Zi Hao Liu, Julie D Forman-Kay, Teresa Head-Gordon

Subjects: Biomolecules (q-bio.BM)

[18] arXiv:2502.12219 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Towards Efficient Molecular Property Optimization with Graph Energy Based Models Show Chinese title

Title: 基于图能量模型的分子性质优化高效方法

Luca Miglior, Lorenzo Simone, Marco Podda, Davide Bacciu

Comments: Accepted at ESANN 2025

Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)

[19] arXiv:2502.15645 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Engineered Zwitterion-Infused Clay Composites with Antibacterial and Antifungal Efficacy Show Chinese title

Title: 工程化的两性离子浸润粘土复合材料及其抗菌和抗真菌功效

Suvash Ghimire, Yi Wu, Manjyot Kaur Chug, Elizabeth J. Brisbois, Kyungtae Kim, Kausik Mukhopadhyay

Subjects: Biomolecules (q-bio.BM)

[20] arXiv:2502.16378 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Auto-ADMET: An Effective and Interpretable AutoML Method for Chemical ADMET Property Prediction Show Chinese title

Title: Auto-ADMET：一种用于化学ADMET属性预测的有效且可解释的自动机器学习方法

Alex G. C. de Sá, David B. Ascher

Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)

[21] arXiv:2502.17449 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Non-Markovain Quantum State Diffusion for the Tunneling in SARS-COVID-19 virus Show Chinese title

Title: 非马尔可夫量子态扩散在SARS-COVID-19病毒隧穿中的应用

Muhammad Waqas Haseeb, Mohamad Toutounji

Comments: 11 pages,5 figures

Subjects: Biomolecules (q-bio.BM)

[22] arXiv:2502.17504 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Protein Large Language Models: A Comprehensive Survey Show Chinese title

Title: 蛋白质大型语言模型：综合综述

Yijia Xiao, Wanjia Zhao, Junkai Zhang, Yiqiao Jin, Han Zhang, Zhicheng Ren, Renliang Sun, Haixin Wang, Guancheng Wan, Pan Lu, Xiao Luo, Yu Zhang, James Zou, Yizhou Sun, Wei Wang

Comments: 24 pages, 4 figures, 5 tables

Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Computational Engineering, Finance, and Science (cs.CE) ; Computation and Language (cs.CL) ; Machine Learning (cs.LG)

[23] arXiv:2502.18875 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation Show Chinese title

Title: 针对目标蛋白降解的SE(3)-等变三元复杂数预测

Fanglei Xue, Meihan Zhang, Shuqi Li, Xinyu Gao, James A. Wohlschlegel, Wenbing Huang, Yi Yang, Weixian Deng

Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)

[24] arXiv:2502.19391 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Towards More Accurate Full-Atom Antibody Co-Design Show Chinese title

Title: 迈向更精确的全原子抗体共设计

Jiayang Wu, Xingyi Zhang, Xiangyu Dong, Kun Xie, Ziqi Liu, Wensheng Gan, Sibo Wang, Le Song

Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)

[25] arXiv:2502.19395 (cross-list from q-bio.BM) [cn-pdf, pdf, html, other]

Title: Fast and Accurate Antibody Sequence Design via Structure Retrieval Show Chinese title

Title: 通过结构检索的抗体序列快速准确设计

Xingyi Zhang, Kun Xie, Ningqiao Huang, Wei Liu, Peilin Zhao, Sibo Wang, Kangfei Zhao, Biaobin Jiang

Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)

[26] arXiv:2502.01461 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration Show Chinese title

Title: 基于对接感知的注意力机制：通过分子上下文集成动态蛋白质表示

Amitay Sicherman, Kira Radinsky

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)

[27] arXiv:2502.01533 (cross-list from cs.LG) [cn-pdf, pdf, other]

Title: Transformers trained on proteins can learn to attend to Euclidean distance Show Chinese title

Title: 在蛋白质上训练的Transformer可以学会关注欧几里得距离

Isaac Ellmen, Constantin Schneider, Matthew I.J. Raybould, Charlotte M. Deane

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[28] arXiv:2502.02552 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Hierarchical Sparse Bayesian Multitask Model with Scalable Inference for Microbiome Analysis Show Chinese title

Title: 用于微生物组分析的分层稀疏贝叶斯多任务模型及其可扩展推理方法

Haonan Zhu, Andre R. Goncalves, Camilo Valdes, Hiranmayi Ranganathan, Boya Zhang, Jose Manuel Martí, Car Reen Kok, Monica K. Borucki, Nisha J. Mulakken, James B. Thissen, Crystal Jaing, Alfred Hero, Nicholas A. Be

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM) ; Applications (stat.AP) ; Computation (stat.CO) ; Methodology (stat.ME)

[29] arXiv:2502.02810 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization Show Chinese title

Title: Mol-LLM：具有改进图利用的多模态通用分子大语言模型

Chanhui Lee, Hanbum Ko, Yuheon Song, YongJun Jeong, Rodrigo Hormazabal, Sehui Han, Kyunghoon Bae, Sungbin Lim, Sungwoong Kim

Comments: 9 pages, 5 figures

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Chemical Physics (physics.chem-ph) ; Biomolecules (q-bio.BM)

[30] arXiv:2502.06634 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language Show Chinese title

Title: 自动标注增强提升分子与自然语言之间的翻译

Zhiqiang Zhong, Simon Sataa-Yu Larsen, Haoyu Guo, Tao Tang, Kuangyu Zhou, Davide Mottin

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[31] arXiv:2502.06846 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure Show Chinese title

Title: Prot2Chat：具有文本、序列和结构早期融合的蛋白质大语言模型

Zhicong Wang, Zicheng Ma, Ziqiang Cao, Changlong Zhou, Jun Zhang, Yiqin Gao

Comments: 8 pages, 3 figures

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[32] arXiv:2502.07237 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: DrugImproverGPT: A Large Language Model for Drug Optimization with Fine-Tuning via Structured Policy Optimization Show Chinese title

Title: DrugImproverGPT：一种用于药物优化的大语言模型并通过结构化策略优化微调

Xuefeng Liu, Songhao Jiang, Siyu Chen, Zhuoran Yang, Yuxin Chen, Ian Foster, Rick Stevens

Subjects: Machine Learning (cs.LG) ; Computation and Language (cs.CL) ; Biomolecules (q-bio.BM) ; Machine Learning (stat.ML)

[33] arXiv:2502.08975 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunities Show Chinese title

Title: 通过深度学习的图结构小分子药物发现：进展、挑战与机遇

Kun Li, Yida Xiong, Hongzhi Zhang, Xiantao Cai, Jia Wu, Bo Du, Wenbin Hu

Comments: 10 pages, 1 figures, 8 tables

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)

[34] arXiv:2502.09135 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Interpreting and Steering Protein Language Models through Sparse Autoencoders Show Chinese title

Title: 通过稀疏自编码器解释和引导蛋白质语言模型

Edith Natalia Villegas Garcia, Alessio Ansuini

Comments: 11 pages, 6 figures

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)

[35] arXiv:2502.09775 (cross-list from q-bio.QM) [cn-pdf, pdf, html, other]

Title: CellFlux: Simulating Cellular Morphology Changes via Flow Matching Show Chinese title

Title: CellFlux：通过流匹配模拟细胞形态变化

Yuhui Zhang, Yuchang Su, Chenyu Wang, Tianhong Li, Zoe Wefers, Jeffrey Nirschl, James Burgess, Daisy Ding, Alejandro Lozano, Emma Lundberg, Serena Yeung-Levy

Comments: Published at ICML 2025

Subjects: Quantitative Methods (q-bio.QM) ; Computer Vision and Pattern Recognition (cs.CV) ; Machine Learning (cs.LG) ; Biomolecules (q-bio.BM) ; Cell Behavior (q-bio.CB)

[36] arXiv:2502.10631 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: ControllableGPT: A Ground-Up Designed Controllable GPT for Molecule Optimization Show Chinese title

Title: 可控制GPT：专为分子优化设计的可控制GPT

Xuefeng Liu, Songhao Jiang, Bo Li, Rick Stevens

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[37] arXiv:2502.11894 (cross-list from cond-mat.soft) [cn-pdf, pdf, other]

Title: AI-guided transition path sampling of lipid flip-flop and membrane nanoporation Show Chinese title

Title: 人工智能引导的脂质翻转和膜纳米孔道采样路径

Matthias Post, Gerhard Hummer

Subjects: Soft Condensed Matter (cond-mat.soft) ; Biomolecules (q-bio.BM)

[38] arXiv:2502.12049 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Classifying the Stoichiometry of Virus-like Particles with Interpretable Machine Learning Show Chinese title

Title: 用可解释的机器学习分类病毒样颗粒的化学计量学

Jiayang Zhang, Xianyuan Liu, Wei Wu, Sina Tabakhi, Wenrui Fan, Shuo Zhou, Kang Lan Tee, Tuck Seng Wong, Haiping Lu

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM) ; Quantitative Methods (q-bio.QM)

[39] arXiv:2502.12453 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: UniMatch: Universal Matching from Atom to Task for Few-Shot Drug Discovery Show Chinese title

Title: UniMatch：从原子到任务的通用少样本药物发现匹配方法

Ruifeng Li, Mingqian Li, Wei Liu, Yuhua Zhou, Xiangxin Zhou, Yuan Yao, Qiang Zhang, Hongyang Chen

Comments: accepted as ICLR 2025 Spotlight

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[40] arXiv:2502.12479 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: MotifBench: A standardized protein design benchmark for motif-scaffolding problems Show Chinese title

Title: MotifBench：一种标准化的基序-支架问题蛋白设计基准

Zhuoqi Zheng, Bo Zhang, Kieran Didi, Kevin K. Yang, Jason Yim, Joseph L. Watson, Hai-Feng Chen, Brian L. Trippe

Comments: Associated content available at github.com/blt2114/MotifBench

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)

[41] arXiv:2502.12638 (cross-list from q-bio.QM) [cn-pdf, pdf, html, other]

Title: NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Show Chinese title

Title: NExT-Mol：三维扩散结合一维语言建模用于三维分子生成

Zhiyuan Liu, Yanchen Luo, Han Huang, Enzhi Zhang, Sihang Li, Junfeng Fang, Yaorui Shi, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua

Comments: ICLR 2025, 10 pages

Subjects: Quantitative Methods (q-bio.QM) ; Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)

[42] arXiv:2502.13344 (cross-list from cs.LG) [cn-pdf, pdf, other]

Title: K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction Show Chinese title

Title: K-Paths：用于药物重定位和药物相互作用预测的图路径推理

Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak, Ghulam Murtaza, Stephen H. Bach, Carsten Eickhoff, Ritambhara Singh

Journal-ref: Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2 (KDD '25), August 3--7, 2025, Toronto, ON, Canada

Subjects: Machine Learning (cs.LG) ; Computation and Language (cs.CL) ; Biomolecules (q-bio.BM)

[43] arXiv:2502.14239 (cross-list from cond-mat.mtrl-sci) [cn-pdf, pdf, other]

Title: Investigating the Optical and Thermodynamic Properties of 2D MoGe2P4 : Potential Material for Photothermal Therapy Show Chinese title

Title: 研究二维 MoGe₂P₄ 的光学和热力学性质：光热疗法的潜在材料

Sudipta Saha, Arpan Sur, Labonno Saha, Md. Kawsar Alam

Subjects: Materials Science (cond-mat.mtrl-sci) ; Biomolecules (q-bio.BM)

[44] arXiv:2502.14555 (cross-list from cond-mat.soft) [cn-pdf, pdf, html, other]

Title: The diffusive dynamics and electrochemical regulation of weak polyelectrolytes across liquid interfaces Show Chinese title

Title: 弱聚电解质在液-液界面的扩散动力学与电化学调控

Giulia Laura Celora, Ralf Blossey, Andreas Munch, Barbara Wagner

Subjects: Soft Condensed Matter (cond-mat.soft) ; Adaptation and Self-Organizing Systems (nlin.AO) ; Pattern Formation and Solitons (nlin.PS) ; Biomolecules (q-bio.BM)

[45] arXiv:2502.16189 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Co-evolution-based Metal-binding Residue Prediction with Graph Neural Networks Show Chinese title

Title: 基于协同进化的金属结合残基预测与图神经网络

Sayedmohammadreza Rastegari, Sina Tabakhi, Xianyuan Liu, Wei Sang, Haiping Lu

Comments: 7 pages, 3 figures

Subjects: Machine Learning (cs.LG) ; Materials Science (cond-mat.mtrl-sci) ; Biomolecules (q-bio.BM) ; Quantitative Methods (q-bio.QM)

[46] arXiv:2502.16270 (cross-list from stat.ME) [cn-pdf, pdf, html, other]

Title: Constrained Shape Analysis with Applications to RNA Structure Show Chinese title

Title: 受限形状分析及其在RNA结构中的应用

Kanti V. Mardia, Benjamin Eltzner, Stephan F. Huckemann

Comments: 33 pages, 9 figures

Subjects: Methodology (stat.ME) ; Computational Engineering, Finance, and Science (cs.CE) ; Biomolecules (q-bio.BM)

[47] arXiv:2502.16446 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation Show Chinese title

Title: 辅助判别器序列生成对抗网络（ADSeqGAN）用于少样本分子生成

Haocheng Tang, Jing Long, Beihong Ji, Junmei Wang

Comments: Accepted by Journal of Chemical Information and Modeling, ASAP

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Biomolecules (q-bio.BM)

[48] arXiv:2502.17233 (cross-list from physics.chem-ph) [cn-pdf, pdf, html, other]

Title: Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations Show Chinese title

Title: Λ-ABF-OPES：阿尔化学自由能计算中更快的收敛与高精度

Narjes Ansari, Zhifeng Francis Jing, Antoine Gagelin, Florent Hédin, Félix Aviat, Jérôme Hénin, Jean-Philip Piquemal, Louis Lagardère

Subjects: Chemical Physics (physics.chem-ph) ; Biomolecules (q-bio.BM)

[49] arXiv:2502.17628 (cross-list from q-bio.QM) [cn-pdf, pdf, html, other]

Title: Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold Show Chinese title

Title: G蛋白偶联受体通过AlphaFold生成的构象状态表征

Garima Chib, Parisa Mollaei, Amir Barati Farimani

Subjects: Quantitative Methods (q-bio.QM) ; Biomolecules (q-bio.BM)

[50] arXiv:2502.19173 (cross-list from cs.LG) [cn-pdf, pdf, other]

Title: A Model-Centric Review of Deep Learning for Protein Design Show Chinese title

Title: 基于模型的深度学习在蛋白质设计中的综述

Gregory W. Kyro, Tianyin Qiu, Victor S. Batista

Subjects: Machine Learning (cs.LG) ; Biomolecules (q-bio.BM)