MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language

Authors: Shoshan, Yoel, Raboh, Moshiko, Ozery-Flato, Michal, Ratner, Vadim, Golts, Alex, Weber, Jeffrey K., Barkan, Ella, Rabinovici-Cohen, Simona, Polaczek, Sagi, Amos, Ido, Shapira, Ben, Hazan, Liam, Ninio, Matan, Ravid, Sivan, Danziger, Michael M., Morrone, Joseph A., Suryanarayanan, Parthasarathy, Rosen-Zvi, Michal, Hexter, Efrat

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2410.22367

Multi-view biomedical foundation models for molecule-target and property prediction

Authors: Suryanarayanan, Parthasarathy, Qiu, Yunguang, Sethi, Shreyans, Mahajan, Diwakar, Li, Hongyang, Yang, Yuxin, Eyigoz, Elif, Saenz, Aldo Guzman, Platt, Daniel E., Rumbell, Timothy H., Ng, Kenney, Dey, Sanjoy, Burch, Myson, Kwon, Bum Chul, Meyer, Pablo, Cheng, Feixiong, Hu, Jianying, Morrone, Joseph A.

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2410.19704

Towards quantum-enabled cell-centric therapeutics

Authors: Basu, Saugata, Born, Jannis, Bose, Aritra, Capponi, Sara, Chalkia, Dimitra, Chan, Timothy A, Doga, Hakan, Flother, Frederik F., Getz, Gad, Goldsmith, Mark, Gujarati, Tanvi, Guzman-Saenz, Aldo, Iliopoulos, Dimitrios, Jones, Gavin O., Knecht, Stefan, Madan, Dhiraj, Maniscalco, Sabrina, Mariella, Nicola, Morrone, Joseph A., Najafi, Khadijeh, Pati, Pushpak, Platt, Daniel, Rapsomaniki, Maria Anna, Ray, Anupama, Rhrissorrakrai, Kahn, Shehab, Omar, Tavernelli, Ivano, Tolunay, Meltem, Utro, Filippo, Woerner, Stefan, Zhuk, Sergiy, Garcia, Jeannette M., Parida, Laxmi

Subject Terms: Quantum Physics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2307.05734

Roughness of molecular property landscapes and its impact on modellability

Authors: Aldeghi, Matteo, Graff, David E., Frey, Nathan, Morrone, Joseph A., Pyzer-Knapp, Edward O., Jordan, Kirk E., Coley, Connor W.

Source: J. Chem. Inf. Model. 2022, 62, 19, 4660-4671

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2207.09250

Self-focusing virtual screening with active design space pruning

Authors: Graff, David E., Aldeghi, Matteo, Morrone, Joseph A., Jordan, Kirk E., Pyzer-Knapp, Edward O., Coley, Connor W.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2205.01753

In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation

Authors: Kang, Seung-gu, Weber, Jeffrey K., Morrone, Joseph A., Zhang, Leili, Huynh, Tien, Cornell, Wendy D.

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Machine Learning, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2204.02513

Analysis of training and seed bias in small molecules generated with a conditional graph-based variational autoencoder -- Insights for practical AI-driven molecule generation

Authors: Kang, Seung-gu, Morrone, Joseph A., Weber, Jeffrey K., Cornell, Wendy D.

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Machine Learning, Physics - Biological Physics

Access URL: http://arxiv.org/abs/2107.08987

Combining docking pose rank and structure with deep learning improves protein-ligand binding mode prediction

Authors: Morrone, Joseph A., Weber, Jeffrey K., Huynh, Tien, Luo, Heng, Cornell, Wendy D.

Subject Terms: Quantitative Biology - Biomolecules, Physics - Biological Physics, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/1910.02845

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity.

Authors: Weber, Jeffrey K¹ (AUTHOR) jkweber@us.ibm.com, Morrone, Joseph A¹ (AUTHOR), Kang, Seung-gu¹ (AUTHOR), Zhang, Leili¹ (AUTHOR), Lang, Lijun¹ (AUTHOR), Chowell, Diego² (AUTHOR), Krishna, Chirag³ (AUTHOR), Huynh, Tien¹ (AUTHOR), Parthasarathy, Prerana^4,5 (AUTHOR), Luan, Binquan¹ (AUTHOR), Alban, Tyler J^4,5 (AUTHOR), Cornell, Wendy D¹ (AUTHOR), Chan, Timothy A^4,5,6,7,8 (AUTHOR) jkweber@us.ibm.com

Source: Briefings in Bioinformatics. Jan2024, Vol. 25 Issue 1, p1-12. 12p.

Subject Terms: *T cell receptors, *HISTOCOMPATIBILITY class I antigens, *MOLECULAR dynamics, *IMMUNE response, *MAJOR histocompatibility complex

Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder—Insights for Practical Al-Driven Molecule Generation

Authors: Kang, Seung-gu, Morrone, Joseph A., Weber, Jeffrey K., Cornell, Wendy D.

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(4):801-816

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632701434&indx=1&recIds=ETOCRN632701434

The role of water and steric constraints in the kinetics of cavity-ligand unbinding

Authors: Tiwary, Pratyush, Mondal, Jagannath, Morrone, Joseph A., Berne, B. J.

Subject Terms: Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics, Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1507.02985

How hydrophobic drying forces impact the kinetics of molecular recognition

Authors: Mondal, Jagannath, Morrone, Joseph A., Berne, B. J.

Source: Proc. Natl. Acad. Sci. USA 110, 13277 (2013)

Subject Terms: Condensed Matter - Soft Condensed Matter, Condensed Matter - Statistical Mechanics, Physics - Biological Physics

Access URL: http://arxiv.org/abs/1305.7505

Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?

Authors: Li, Jingyuan, Morrone, Joseph A., Berne, B. J.

Subject Terms: Condensed Matter - Soft Condensed Matter, Condensed Matter - Statistical Mechanics, Physics - Biological Physics

Access URL: http://arxiv.org/abs/1208.6170

Theory and simulations of quantum glass forming liquids

Authors: Markland, Thomas E., Morrone, Joseph A., Miyazaki, Kunimasa, Berne, Bruce J., Reichman, David R., Rabani, Eran

Subject Terms: Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1111.4191

Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes

Authors: Morrone, Joseph A., Li, Jingyuan, Berne, B. J.

Subject Terms: Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/1110.0862

Momentum distribution, vibrational dynamics and the potential of mean force in ice

Authors: Lin, Lin, Morrone, Joseph A., Car, Roberto, Parrinello, Michele

Subject Terms: Quantum Physics, Condensed Matter - Statistical Mechanics, Physics - Chemical Physics

Access URL: http://arxiv.org/abs/1102.0804

Combining Docking Pose Rank and Structure with Deep Learning Improves Protein—Ligand Binding Mode Prediction over a Baseline Docking Approach

Authors: Morrone, Joseph A., Weber, Jeffrey K., Huynh, Tien, Luo, Heng, Cornell, Wendy D.

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 60(9):4170-4179

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632690033&indx=1&recIds=ETOCRN632690033

Quantum fluctuations can promote or inhibit glass formation

Authors: Markland, Thomas E., Morrone, Joseph A., Berne, B. J., Miyazaki, Kunimasa, Rabani, Eran, Reichman, David R.

Subject Terms: Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/1011.0015

Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

Authors: Morrone, Joseph A., Markland, Thomas E., Ceriotti, Michele, Berne, B. J.

Source: J. Chem. Phys. 134, 014103 (2011)

Subject Terms: Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/1008.5377

Displaced path integral formulation for the momentum distribution of quantum particles

Authors: Lin, Lin, Morrone, Joseph, Car, Roberto, Parrinello, Michele

Source: Phys.Rev.Lett.105:110602,2010

Subject Terms: Physics - Computational Physics, Quantum Physics

Access URL: http://arxiv.org/abs/1004.0868