Biomolecules

Authors and titles for q-bio.BM in Apr 2024

[1]  arXiv:2404.00081 [pdf, ps, other]

Title: Molecular Generative Adversarial Network with Multi-Property Optimization

Authors: Huidong Tang, Chen Li, Sayaka Kamei, Yoshihiro Yamanishi, Yasuhiko Morimoto

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

[2]  arXiv:2404.01405 [pdf, ps, other]

Title: The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding

Authors: Olympia-Dialekti Vouzina, Alexandros Tafanidis, Nicholas M. Glykos

Subjects: Biomolecules (q-bio.BM)

[3]  arXiv:2404.02789 [pdf, ps, other]

Title: RNA Dynamics from Experimental and Computational Approaches

Authors: Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka, Michael Sattler, Hashim M. Al-Hashimi, Pascal Auffinger, Maria Duca, Yann Foricher, Danny Incarnato, Alisha N. Jones, Serdal Kirmizialtin, Miroslav Krepl, Modesto Orozco, Giulia Palermo, Samuela Pasquali, Loïc Salmon, Harald Schwalbe, Eric Westhof, Martin Zacharias

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

[4]  arXiv:2404.02909 [pdf, other]

Title: A Comprehensive System for Secondary Structure Analysis of Protein Models

Authors: Vedh Kannan

Subjects: Biomolecules (q-bio.BM)

[5]  arXiv:2404.05329 [pdf, ps, other]

Title: In silico bioactivity prediction of proteins interacting with graphene-based nanomaterials guides rational design of biosensor

Authors: Jing Ye, Minzhi Fan, Xiaoyu Zhang, Shasha Lu, Mengyao Chai, Yunshan Zhang, Xiaoyu Zhao, Shuang Li, Diming Zhang

Subjects: Biomolecules (q-bio.BM)

[6]  arXiv:2404.06481 [pdf, other]

Title: GeoDirDock: Guiding Docking Along Geodesic Paths

Authors: Raúl Miñán, Javier Gallardo, Álvaro Ciudad, Alexis Molina

Comments: Generative and Experimental Perspectives for Biomolecular Design Workshop at ICLR 2024

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

[7]  arXiv:2404.06691 [pdf, ps, other]

Title: Latent Chemical Space Searching for Plug-in Multi-objective Molecule Generation

Authors: Ningfeng Liu (1 and 2), Jie Yu (1), Siyu Xiu (1), Xinfang Zhao (1), Siyu Lin (1), Bo Qiang (1), Ruqiu Zheng (1), Hongwei Jin (1), Liangren Zhang (1), Zhenming Liu (1 and 3) ((1) State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, (2) Peking-Tsinghua Center for Life Science (CLS), Peking University, (3) State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University)

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)

[8]  arXiv:2404.07852 [pdf, ps, other]

Title: A New Route for the Determination of Protein Structure and Function

Authors: S. H. Mejias, A. L. Cortajarena, R. Mincigrucci, C. Svetina, C. Masciovecchio

Subjects: Biomolecules (q-bio.BM)

[9]  arXiv:2404.09738 [pdf, ps, other]

Title: AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

Authors: Kewei Li, Yuqian Wu, Yutong Guo, Yinheng Li, Yusi Fan, Ruochi Zhang, Lan Huang, Fengfeng Zhou

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

[10]  arXiv:2404.10178 [pdf, other]

Title: CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders

Authors: Chentianye Xu, Xueying Zhan, Min Xu

Subjects: Biomolecules (q-bio.BM); Computer Vision and Pattern Recognition (cs.CV)

[11]  arXiv:2404.10260 [pdf, other]

Title: HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights

Authors: Xiaomin Fang, Jie Gao, Jing Hu, Lihang Liu, Yang Xue, Xiaonan Zhang, Kunrui Zhu

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

[12]  arXiv:2404.11199 [pdf, other]

Title: RiboDiffusion: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models

Authors: Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li

Comments: 15 pages

Subjects: Biomolecules (q-bio.BM)

[13]  arXiv:2404.12141 [pdf, other]

Title: MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space

Authors: Yanru Qu, Keyue Qiu, Yuxuan Song, Jingjing Gong, Jiawei Han, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

Comments: 20 pages, 11 figures

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

[14]  arXiv:2404.12565 [pdf, other]

Title: Limits on Inferring T-cell Specificity from Partial Information

Authors: James Henderson, Yuta Nagano, Martina Milighetti, Andreas Tiffeau-Mayer

Comments: 24 pages, 15 figures

Subjects: Biomolecules (q-bio.BM); Statistical Mechanics (cond-mat.stat-mech); Information Theory (cs.IT)

[15]  arXiv:2404.14353 [pdf, ps, other]

Title: Electroporation-mediated Metformin for effective anticancer treatment of triple-negative breast cancer cells

Authors: Praveen Sahu, Ignacio G. Camarillo, Pragatheiswar Giri, Raji Sundararajan

Subjects: Biomolecules (q-bio.BM); Cell Behavior (q-bio.CB)

[16]  arXiv:2404.14821 [pdf, other]

Title: Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction

Authors: Valerio Piomponi, Miroslav Krepl, Jiri Sponer, Giovanni Bussi

Subjects: Biomolecules (q-bio.BM)

[17]  arXiv:2404.15805 [pdf, other]

Title: Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering

Authors: Shujian Jiao, Bingxuan Li, Lei Wang, Xiaojin Zhang, Wei Chen, Jiajie Peng, Zhongyu Wei

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

[18]  arXiv:2404.18785 [pdf, other]

Title: DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution

Authors: Paolo Rissone, Marc Rico-Pasto, Steve Smith, Felix Ritort

Comments: Main: 23 pages, 4 figures, 1 table SI: 13 pages, 7 figures, 5 tables

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

[19]  arXiv:2404.19230 [pdf, ps, other]

Title: Deep Lead Optimization: Leveraging Generative AI for Structural Modification

Authors: Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Yuansheng Huang, Dejun Jiang, Chang-yu Hsieh, Peichen Pan, Tingjun Hou

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

[20]  arXiv:2404.19739 [pdf, other]

Title: Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation

Authors: Ian Dunn, David Ryan Koes

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

[21]  arXiv:2404.00110 (cross-list from q-bio.PE) [pdf, ps, other]

Title: Microbial assessment in a rare Norwegian book collection: a One Health approach to cultural heritage

Authors: Sílvia O. Sequeira, Ekaterina Pasnak, Carla Viegas, Bianca Gomes, Marta Dias, Renata Cervantes, Pedro Pena, Magdalena Twarużek, Robert Kosicki, Susana Viegas, Liliana Aranha Caetano, Maria João Penetra, Inês Santos, Ana Teresa Caldeira, Catarina Pinheiro

Comments: 17 pages, 7 figures, 2 tables

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

[22]  arXiv:2404.04041 (cross-list from q-bio.PE) [pdf, ps, other]

Title: The Origin of Mutational Epistasis

Authors: Jorge A. Vila

Comments: 19 pages, 1 figure

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

[23]  arXiv:2404.08711 (cross-list from q-bio.QM) [pdf, ps, other]

Title: Drug Repurposing for Parkinson's Disease Using Random Walk With Restart Algorithm and the Parkinson's Disease Ontology Database

Authors: Pratham Kankariya, Rachita Rode, Kevin Mudaliar, Prof. Pranali Hatode

Comments: 5 pages, Final Year Engineering Project on Machine Learning and Healthcare Industry

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

[24]  arXiv:2404.12029 (cross-list from q-bio.QM) [pdf, other]

Title: KnotResolver: Tracking self-intersecting filaments in microscopy using directed graphs

Authors: Dhruv Khatri, Shivani A. Yadav, Chaitanya A. Athale

Comments: Manuscript in submission

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

[25]  arXiv:2404.16196 (cross-list from q-bio.QM) [pdf, other]

Title: ApisTox: a new benchmark dataset for the classification of small molecules toxicity on honey bees

Authors: Jakub Adamczyk, Jakub Poziemski, Paweł Siedlecki

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