BPS2025 Full Program

1521-Pos Board B528 ATOMISTIC INSIGHTS INTO HOMEODOMAIN DNA TARGET RECOGNI TION: UNVEILING THE ROLES OF HELICES AND INTRINSICALLY DIS ORDERED REGIONS THROUGH MILLISECOND-SCALE ALL-ATOM MD SIMULATIONS. Jejoong Yoo Computational Methods and Machine Learning, Artificial Intelligence, and Bioinformatics for Inference (Boards B529 - B563) 1522-Pos Board B529 COMPARISON OF PREDICTED LIGAND BINDING POSES INFORMS PRO TEIN STRUCTURAL MODEL SELECTION. Masha Karelina , Ron O. Dror 1523-Pos Board B530 MACHINE LEARNING MODELS FOR THE PREDICTION OF PROTEIN DYNAMICS AT DIFFERENT STAGES OF EVOLUTION. Michael A. Sauer , Christopher Shin, Souvik Mondal, Matthias Heyden 1524-Pos Board B531 MODELING REVEALS THE STRENGTH OF WEAK INTERACTIONS IN STACKED TRIMERIC RING ASSEMBLY. Leonila Lagunes 1525-Pos Board B532 COARSE-GRAINED SIMULATIONS OF HIV MATURATION WITHIN VIRAL PARTICLES. Sinai Lee , Ethan Wang, Alvin Yu 1526-Pos Board B533 MOLECULAR INSIGHTS INTO COLD-ADAPTED BETA-GLUCOSIDASES. Dulitha Prasanna Kulathunga , Davit Potoyan 1527-Pos Board B534 PREDICTING PROTEIN ADSORPTION AND ENRICHMENT ON NANOPARTI CLES USING RANDOM FOREST MODELS WITH NANOPARTICLE, PROTEIN, AND EXPERIMENTAL FEATURES. Nicole Vijgen , Karsten M. Poulsen, Gustavo Sosa Macias, Christine K. Payne 1528-Pos Board B535 AI-DRIVEN ANTIMICROBIAL-PEPTIDE DISCOVERY AND OPTIMIZATION WITH INPUTS FROM HIGH-THROUGHPUT EXPERIMENTATION AND MO LECULAR DYNAMICS SIMULATIONS. Kinjal Mondal , Sarala Padi, Navleen Kaur, Antonio Cardone, Ella Mihailescu, Jeffery B. Klauda 1529-Pos Board B536 Travel Award Winner MOLECULAR DESIGN WITH GENERATIVE AI: A TRANSFORMER GRAPH VARIATIONAL AUTOENCODER APPROACH. Trieu Nguyen , Aleksandra M. Karolak 1530-Pos Board B537 OVERCOMING EXTRAPOLATION CHALLENGES OF DEEP LEARNING BY INCORPORATING PHYSICS IN PROTEIN SEQUENCE-FUNCTION MODEL ING. Shrishti Barethiya , Jian Huang, Xiao Liu, Hui Guan, Jianhan Chen 1531-Pos Board B538 Canceled COMPUTATIONAL PROTEIN DESIGN FOR A NOVEL POROUS DNA-PRO TEIN CO-CRYSTAL. Emma N. Magna , Christopher D. Snow 1532-Pos Board B539 MULTI-EGO: ACCURATE AND EFFICIENT MODELLING OF BIOMOLECULAR SELF-ASSEMBLY PROCESSES. Carlo Camilloni 1533-Pos Board B540 PHYSICS-GUIDED DEEP GENERATIVE MODEL FOR NEW LIGAND DISCOV ERY ABSTRACT. Nikhil Dhiman , Uriel Baldesco, Dikshant Sagar, Negin Board B541 GRAPH-BASED SIMILARITY FOR IONIZABLE RESIDUES: COMMUNITY DETECTION FOR TARGETED PKA MEASUREMENTS. Ada Y. Chen , Janez Konc, Ana Damjanovic, Bernard R. Brooks Forouzesh 1534-Pos

1535-Pos Board B542 ADVANCED DEEP LEARNING MODEL TO PREDICT DNA-DNA BINDING INTERACTIONS. Karishma R. Matange , Gunavaran Brihadiswaran, Kyle J. Tomek, James M. Tuck, Albert J. Keung 1536-Pos Board B543 Travel Award Winner RECENT DEVELOPMENTS IN INTEGRATIVE STRUCTURAL MODELING OF MACROMOLECULAR ASSEMBLIES. Shruthi Viswanath 1537-Pos Board B544 A NOVEL APPROACH TO GLYCAN ENSEMBLE DESIGN THROUGH COM BINATORIAL OPTIMIZATION AND STRUCTURAL CHARACTERIZATION IN SILICO. Jason D. Kantorow , Shashi Murthy, Srirupa Chakraborty 1538-Pos Board B545 HOW PROTEIN STRUCTURES AFFECT ESM3’S BINDING AFFINITY PREDIC TIONS. Thomas Loux, Dianzhuo Wang , Eugene Shakhnovich 1539-Pos Board B546 A UNIFIED PRE-TRAINED RNA FOUNDATION MODEL FOR DISSECTING AND ENGINEERING RNA MOLECULES. Han Wen 1540-Pos Board B547 AUTOMATED STRUCTURE-BASED DRUG DESIGN WITH GENERATIVE DEEP LEARNING. Jesse Weller , Remo Rohs 1541-Pos Board B548 RNA STRUCTURE PREDICTION VIA DEEP LEARNING DESPITE DATA SPAR SITY. Alexander Schug 1542-Pos Board B549 PREDICTING NERVE AGENT TOXICITY USING MACHINE LEARNING. Keunhong Jeong 1543-Pos Board B550 FROM MOLECULAR CHAOS TO CLARITY: A DEEP GENERATIVE MODEL TO DECIPHER COMPLEX MOLECULAR PATHWAYS. Yingwen Huang , Hong kang Zhu, Ioana C. Butu, Ben O’Shaughnessy 1544-Pos Board B551 DEEP LEARNING APPROACHES FOR PROTEIN DYNAMICS EXTRACTION FROM CRYO-EM MAPS AND STRUCTURE-BASED DE NOVO MOLECU LAR GENERATION. Mitsugu Araki , Shigeyuki Matsumoto, Biao Ma, Kei Terayama, Yasushi Okuno 1545-Pos Board B552 RFDIFFUSION AND MD SIMULATIONS: CRAFTING PEPTIDES TO OUT SMART ALZHEIMER’S DISEASE. Vincent Nieto , Nils A. Berglund, Malene Overby 1546-Pos Board B553 COMPUTATIONAL IDENTIFICATION AND IN VITRO VALIDATION OF DI VERSE NOVEL COMPOUNDS TARGETTING MYCOBACTERIUM TUBERCU LOSIS. Ruben E.A. Cloete 1547-Pos Board B554 Travel Award Winner MUTATIONS IN DRUG BINDING SITES: INTEGRATING COMPUTATIONAL CHEMISTRY AND MACHINE LEARNING TO UNDERSTAND MUTATION-IN DUCED RESISTANCE. Katarzyna Mizgalska , Wayne C. Guida, Aleksandra M. Karolak 1549-Pos Board B556 FREE ENERGY MOLECULAR DYNAMICS-BASED ACTIVE LEARNING FOR STRUCTURE-BASED DRUG DESIGN. S. Benjamin Koby , Filipp Gusev, Evgeny Gutkin, Francesco Gentile, Fuqiang Ban, Olexandr Isayev, Artem Cherkasov, Maria G. Kurnikova 1550-Pos Board B557 DEEP-LEARNING STRUCTURE ELUCIDATION FROM SINGLE-MUTANT DEEP MUTATIONAL SCANNING. Steffen Lindert

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