Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics

Wei Chen, Huan He, Jing Wang, Jiahui Wang and Chia-en A. Chang

Phys. Chem. Chem. Phys., 2023, 25, 2098
DOI: 10.1039/D2CP04584B

Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase

Alexandra N. Bogner and John J. Tanner

Org. Biomol. Chem., 2022, 20, 895
DOI: 10.1039/D1OB02328D

Explicit water-ligand docking, drug-likeness and molecular dynamics simulation analysis to predict the potency of Boerhavia diffusa plant extract against mutant wilms tumor-1 protein responsible for type 4 nephrotic syndrome

Sibani Sahu, Maheswata Moharana, Anuradha Das, Biswajit Mishra and Satya Narayan Sahu

Journal of Biomolecular Structure and Dynamics, 2026, 44, 1250
DOI: 10.1080/07391102.2024.2431649

Structural conservation of antibiotic interaction with ribosomes

Helge Paternoga, Caillan Crowe-McAuliffe, Lars V. Bock, Timm O. Koller, Martino Morici, Bertrand Beckert, Alexander G. Myasnikov, Helmut Grubmüller, Jiří Nováček and Daniel N. Wilson

Nat Struct Mol Biol, 2023, 30, 1380
DOI: 10.1038/s41594-023-01047-y

Local Water Content in Polymer Gels Measured with Super‐Resolved Fluorescence Lifetime Imaging

Sankar Jana, Oleksii Nevskyi, Hannah Höche, Leon Trottenberg, Eric Siemes, Jörg Enderlein, Alexandre Fürstenberg and Dominik Wöll

Angew Chem Int Ed, 2024, 63
DOI: 10.1002/anie.202318421

Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition

Arghya P. Ghosh, Julia N. DuVal, Adrianna M. Cavoto and Maria C. Nagan

Current Research in Structural Biology, 2026, 11, 100184
DOI: 10.1016/j.crstbi.2026.100184

Lokaler Wassergehalt in Polymergelen bestimmt über superauflösende Fluoreszenzlebensdauer‐Bildgebung

Sankar Jana, Oleksii Nevskyi, Hannah Höche, Leon Trottenberg, Eric Siemes, Jörg Enderlein, Alexandre Fürstenberg and Dominik Wöll

Angewandte Chemie, 2024, 136
DOI: 10.1002/ange.202318421

Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo

William G. Poole, Marley L. Samways, Davide Branduardi, Richard D. Taylor, Marcel L. Verdonk and Jonathan W. Essex

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-60561-3

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

Galen J. Correy, Daniel W. Kneller, Gwyndalyn Phillips, Swati Pant, Silvia Russi, Aina E. Cohen, George Meigs, James M. Holton, Stefan Gahbauer, Michael C. Thompson, Alan Ashworth, Leighton Coates, Andrey Kovalevsky, Flora Meilleur and James S. Fraser

Sci. Adv., 2022, 8
DOI: 10.1126/sciadv.abo5083

Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery

Laura Almena Rodriguez, Vera A. Spanke and Christian Kersten

J. Chem. Inf. Model., 2025, 65, 12959
DOI: 10.1021/acs.jcim.5c02352

Identification of Novel SGLT‐2 Inhibitors Against Diabetes Mellitus Type 2: A Multiphase Computational Approach

Liu Desen, Huang Hua, Huang Yonghong, Qurban Ali and Gao Daxin

ChemistrySelect, 2025, 10
DOI: 10.1002/slct.202501163

Hydrogen-Bond Donors in Drug Design

Peter W. Kenny

J. Med. Chem., 2022, 65, 14261
DOI: 10.1021/acs.jmedchem.2c01147

Potential energy surfaces of antiparallel water-water interactions

Milan R. Milovanović, Jelena M. Živković, Dragan B. Ninković and Snežana D. Zarić

Journal of Molecular Liquids, 2023, 389, 122758
DOI: 10.1016/j.molliq.2023.122758

Backbone hydration of α -helical peptides: hydrogen-bonding and surface hydrophobicity/hydrophilicity

Ali Eltareb, Janel Rivera-Cancel, Gustavo E. Lopez and Nicolas Giovambattista

Molecular Physics, 2024, 122
DOI: 10.1080/00268976.2024.2323637

Water Networks in Complexes between Proteins and FDA-Approved Drugs

Marley L. Samways, Hannah E. Bruce Macdonald, Richard D. Taylor and Jonathan W. Essex

J. Chem. Inf. Model., 2023, 63, 387
DOI: 10.1021/acs.jcim.2c01225

Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase

Jan Silhan, Martin Klima, Tomas Otava, Petr Skvara, Dominika Chalupska, Karel Chalupsky, Jan Kozic, Radim Nencka and Evzen Boura

Nat Commun, 2023, 14
DOI: 10.1038/s41467-023-38019-1

De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO

Mark Kriegel and Yves A. Muller

Sci Rep, 2023, 13
DOI: 10.1038/s41598-023-43659-w

Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory

Hridoy R. Bairagya, Alvea Tasneem and Debapriyo Sarmadhikari

Proteins, 2024, 92, 735
DOI: 10.1002/prot.26665

Water: new aspect of hydrogen bonding in the solid state

Milan R. Milovanović, Ivana M. Stanković, Jelena M. Živković, Dragan B. Ninković, Michael B. Hall and Snežana D. Zarić

IUCrJ, 2022, 9, 639
DOI: 10.1107/S2052252522006728

Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids

Stephen Neidle

Pharmaceuticals, 2021, 15, 7
DOI: 10.3390/ph15010007

In Silico Evaluation of the Thr58-Associated Conserved Water with KRAS Switch-II Pocket Binders

Renne Leini and Tatu Pantsar

J. Chem. Inf. Model., 2023, 63, 1490
DOI: 10.1021/acs.jcim.2c01479

Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations

Huaxin Zhou, Haohao Fu, Xueguang Shao and Wensheng Cai

J. Chem. Inf. Model., 2023, 63, 7837
DOI: 10.1021/acs.jcim.3c01636

Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm

Kochi Sato and Masayoshi Nakasako

BIOPHYSICS, 2025, 22, n/a
DOI: 10.2142/biophysico.bppb-v22.0004

Absolute Binding Free Energy Calculations for Buried Water Molecules

Yunhui Ge, Hannah M. Baumann and David L. Mobley

J. Chem. Theory Comput., 2022, 18, 6482
DOI: 10.1021/acs.jctc.2c00658

Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities

Anmol Kumar, Himanshu Goel, Wenbo Yu, Mingtian Zhao and Alexander D. MacKerell

J. Chem. Theory Comput., 2024, 20, 11032
DOI: 10.1021/acs.jctc.4c01165

Recent Progress in the Discovery of Anti‐Mpox Agents

Le Wang, Tao Zhang, Na Wang, Xinyong Liu and Dongwei Kang

Medicinal Research Reviews, 2026, 46, 40
DOI: 10.1002/med.70004

Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data

Kochi Sato, Mao Oide and Masayoshi Nakasako

Sci Rep, 2023, 13
DOI: 10.1038/s41598-023-29442-x

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo

Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex and David L. Mobley

J Comput Aided Mol Des, 2022, 36, 767
DOI: 10.1007/s10822-022-00479-w

Leveraging analog quantum computing with neutral atoms for solvent configuration prediction in drug discovery

Mauro D'Arcangelo, Louis-Paul Henry, Loïc Henriet, Daniele Loco, Nicolaï Gouraud, Stanislas Angebault, Jules Sueiro, Jérôme Forêt, Pierre Monmarché and Jean-Philip Piquemal

Phys. Rev. Research, 2024, 6
DOI: 10.1103/PhysRevResearch.6.043020

A greener solution: Spent bleaching earth as a sustainable adsorbent for wastewater treatment

Mansoor Ahmed Kandhro, Sarfaraz Ahmed Mahesar, Mustafa Topkafa, Ilyas Deveci, Saba Naz, Zahid Hussain Shar, Aftab Ahmed Kandhro, Aijaz Ali Otho and Syed Tufail Hussain Sherazi

Journal of Water Process Engineering, 2026, 86, 109919
DOI: 10.1016/j.jwpe.2026.109919

Spatially Resolved Hydration Thermodynamics in Biomolecular Systems

Saumyak Mukherjee and Lars V. Schäfer

J. Phys. Chem. B, 2022, 126, 3619
DOI: 10.1021/acs.jpcb.2c01088

NMR-driven structure-based drug discovery by unveiling molecular interactions

Gerald Platzer, Moriz Mayer, Darryl B. McConnell and Robert Konrat

Commun Chem, 2025, 8
DOI: 10.1038/s42004-025-01542-x

Decoding BCL6 Inhibitors: Computational Insights into the Impact of Water Networks on Potency

Daniella E. Hares, Andrea Scarpino, Michael S. Bodnarchuk and Swen Hoelder

J. Chem. Inf. Model., 2025, 65, 9557
DOI: 10.1021/acs.jcim.5c01188

Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo

Oliver J. Melling, Marley L. Samways, Yunhui Ge, David L. Mobley and Jonathan W. Essex

J. Chem. Theory Comput., 2023, 19, 1050
DOI: 10.1021/acs.jctc.2c00823

Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data

Jelena Tošović, Domagoj Fijan, Marko Jukič and Urban Bren

J. Chem. Inf. Model., 2022, 62, 6105
DOI: 10.1021/acs.jcim.2c00801

Physics-informed machine learning of the correlation functions in bulk fluids

Wenqian Chen, Peiyuan Gao and Panos Stinis

Physics of Fluids, 2024, 36
DOI: 10.1063/5.0175065

Hydrogen bonding blues: Vibrational spectroscopy of the TIP3P water model

Zeke A. Piskulich and Qiang Cui

The Journal of Chemical Physics, 2025, 162
DOI: 10.1063/5.0243509

Water position sampling on protein structures based on a 3D distribution function using a weighted Monte Carlo method

Shinpei Kobayashi, Yasuomi Kiyota and Mayuko Takeda-Shitaka

Bulletin of the Chemical Society of Japan, 2024, 97
DOI: 10.1093/bulcsj/uoae063

Dynamics of nucleoplasm in human leukemia cells: A thrust towards designing anti-leukemic agents

Hridoy R. Bairagya

Journal of Molecular Graphics and Modelling, 2024, 131, 108807
DOI: 10.1016/j.jmgm.2024.108807

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS

Maham Hamid, Muhammad Farhan Khalid, Safee Ullah Chaudhary and Shahid Khan

IJMS, 2022, 23, 12771
DOI: 10.3390/ijms232112771

Molecular docking and dynamics in protein serine/threonine kinase drug discovery: advances, challenges, and future perspectives

Gulam Mustafa Hasan, Taj Mohammad, Sobia Zaidi, Anas Shamsi and Md. Imtaiyaz Hassan

Front. Pharmacol., 2025, 16
DOI: 10.3389/fphar.2025.1696204

The application of WaterMap-guided structure-based virtual screening in novel drug discovery

Agnieszka A. Kaczor, Agata Zięba and Dariusz Matosiuk

Expert Opinion on Drug Discovery, 2024, 19, 73
DOI: 10.1080/17460441.2023.2267015

Biotin’s Lessons in Drug Design

Darryl B. McConnell

J. Med. Chem., 2021, 64, 16319
DOI: 10.1021/acs.jmedchem.1c00975

Enthalpic Classification of Water Molecules in Target–Ligand Binding

Viktor Szél, Balázs Zoltán Zsidó and Csaba Hetényi

J. Chem. Inf. Model., 2024, 64, 6583
DOI: 10.1021/acs.jcim.4c00794

Resolving binding pathways and solvation thermodynamics of plant hormone receptors

Chuankai Zhao, Diego E. Kleiman and Diwakar Shukla

Journal of Biological Chemistry, 2023, 299, 105456
DOI: 10.1016/j.jbc.2023.105456

Quantum Mechanical-Cluster Approach to Solve the Bioisosteric Replacement Problem in Drug Design

Timofey V. Losev, Igor S. Gerasimov, Maria V. Panova, Alexey A. Lisov, Yana R. Abdyusheva, Polina V. Rusina, Eugenia Zaletskaya, Oleg V. Stroganov, Michael G. Medvedev and Fedor N. Novikov

J. Chem. Inf. Model., 2023, 63, 1239
DOI: 10.1021/acs.jcim.2c01212

Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields

Jiahua Deng and Qiang Cui

J. Chem. Theory Comput., 2024, 20, 1897
DOI: 10.1021/acs.jctc.4c00013

The structural differences between mushroom and human tyrosinase cleared by investigating the inhibitory activities of stilbenes

Takahiro Oyama, Atsushi Yoshimori, Haruka Ogawa, Yoko Shirai, Hideaki Abe, Takanori Kamiya and Sei-ichi Tanuma

Journal of Molecular Structure, 2023, 1272, 134180
DOI: 10.1016/j.molstruc.2022.134180

Insights into novel inhibitory compounds against 14–3-3 ε potential cancer therapeutic target through microscopic solvated dynamics

Alaa Abdulaziz Eisa

Journal of Molecular Liquids, 2025, 428, 127541
DOI: 10.1016/j.molliq.2025.127541

Free Energy Density of a Fluid and Its Role in Solvation and Binding

Michael K Gilson and Tom Kurtzman

J. Chem. Theory Comput., 2024, 20, 2871
DOI: 10.1021/acs.jctc.3c01173

Thermodynamic Data Remain a Hot Tip for Decoding Binding Affinity and Water Impact on Protein–Ligand Complex Formation to Assist Lead Optimization

Gerhard Klebe

J. Med. Chem., 2026, 69, 3719
DOI: 10.1021/acs.jmedchem.5c03100

All you need is water: Converging ligand binding simulations with hydration collective variables

Marc Schulze, Tetiana Khakhula, Nicola Piasentin, Simone Aureli, Valerio Rizzi and Francesco Luigi Gervasio

The Journal of Chemical Physics, 2025, 163
DOI: 10.1063/5.0287856