Decoding the limits of deep learning in molecular docking for drug discovery

Yue Li, Jiacai Yi, Hui Li, Kun Li, Fenghua Kang, Youchao Deng, Chengkun Wu, Xiangzheng Fu, Dejun Jiang and Dongsheng Cao

Chem. Sci., 2025, 16, 17374
DOI: 10.1039/D5SC05395A

Theoretical investigation of functional responses of bio-molecular assembly networks

Pankaj Gautam and Sudipta Kumar Sinha

Soft Matter, 2023, 19, 3803
DOI: 10.1039/D2SM01530G

Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects

Imran Sama-ae, Suthinee Sangkanu, Abolghasem Siyadatpanah, Roghayeh Norouzi, Julalak Chuprom, Watcharapong Mitsuwan, Sirirat Surinkaew, Rachasak Boonhok, Alok K. Paul, Tooba Mahboob, Najme Sadat Abtahi, Tajudeen O. Jimoh, Sónia M.R. Oliveira, Madhu Gupta, Chea Sin, Maria de Lourdes Pereira, Polrat Wilairatana, Christophe Wiart, Mohammed Rahmatullah, Karma G. Dolma and Veeranoot Nissapatorn

F1000Res, 2023, 11, 1274
DOI: 10.12688/f1000research.126227.3

Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers

Lyan van der Sleen, Jan A. Stevens, Siewert J. Marrink, Bert Poolman and Kasia Tych

Cell Reports, 2024, 43, 114110
DOI: 10.1016/j.celrep.2024.114110

Rational Design of Protein-Specific Folding Modifiers

Anirban Das, Anju Yadav, Mona Gupta, Purushotham R, Vishram L. Terse, Vicky Vishvakarma, Sameer Singh, Tathagata Nandi, Arkadeep Banerjee, Kalyaneswar Mandal, Shachi Gosavi, Ranabir Das, Sri Rama Koti Ainavarapu and Sudipta Maiti

J. Am. Chem. Soc., 2021, 143, 18766
DOI: 10.1021/jacs.1c09611

Theragnostic Dual‐Action Platform: Ruthenium p‐Cymene‐Derived Metalloantibiotics With NIR‐II Photoacoustic Spectral Signal

Bhumika Agrahari, Kajal Chaudhary, Sayari Dewan, Himanshu Sonker, Arjun S.V, Anshuman Chandra, Nidhi Awasthi, Hanumanthappa Makari, Sanhita Sinharay and Ritika Gautam Singh

Small, 2025, 21
DOI: 10.1002/smll.202503986

Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment

Oliver Brylski, Simon Ebbinghaus and Jonathan W. Mueller

Front. Mol. Biosci., 2019, 6
DOI: 10.3389/fmolb.2019.00031

Exploring the dual effect of novel 1,4-diarylpyranopyrazoles as antiviral and anti-inflammatory for the management of SARS-CoV-2 and associated inflammatory symptoms

Azizah M. Malebari, Hany E. A. Ahmed, Saleh K. Ihmaid, Abdelsattar M. Omar, Yosra A. Muhammad, Sultan S. Althagfan, Naif Aljuhani, Abdel-Aziz A. A. El-Sayed, Ahmed H. Halawa, Heba M. El-Tahir, Safaa A. Turkistani, Mohammed Almaghrabi, Ahmed K. B. Aljohani, Ahmed M. El-Agrody and Hamada S. Abulkhair

Bioorganic Chemistry, 2023, 130, 106255
DOI: 10.1016/j.bioorg.2022.106255

The Svedberg Lecture 2017. From nano to micro: the huge dynamic range of the analytical ultracentrifuge for characterising the sizes, shapes and interactions of molecules and assemblies in Biochemistry and Polymer Science

Stephen E. Harding

Eur Biophys J, 2018, 47, 697
DOI: 10.1007/s00249-018-1321-3

Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects

Imran Sama-ae, Suthinee Sangkanu, Abolghasem Siyadatpanah, Roghayeh Norouzi, Julalak Chuprom, Watcharapong Mitsuwan, Sirirat Surinkaew, Rachasak Boonhok, Alok K. Paul, Tooba Mahboob, Najme Sadat Abtahi, Tajudeen O. Jimoh, Sónia M.R. Oliveira, Madhu Gupta, Chea Sin, Maria de Lourdes Pereira, Polrat Wilairatana, Christophe Wiart, Mohammed Rahmatullah, Karma G. Dolma and Veeranoot Nissapatorn

F1000Res, 2022, 11, 1274
DOI: 10.12688/f1000research.126227.1

Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble

Tushar Modi, Jonathan Huihui, Kingshuk Ghosh and S. Banu Ozkan

Phil. Trans. R. Soc. B, 2018, 373, 20170184
DOI: 10.1098/rstb.2017.0184

Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects

Imran Sama-ae, Suthinee Sangkanu, Abolghasem Siyadatpanah, Roghayeh Norouzi, Julalak Chuprom, Watcharapong Mitsuwan, Sirirat Surinkaew, Rachasak Boonhok, Alok K. Paul, Tooba Mahboob, Najme Sadat Abtahi, Tajudeen O. Jimoh, Sónia M.R. Oliveira, Madhu Gupta, Chea Sin, Maria de Lourdes Pereira, Polrat Wilairatana, Christophe Wiart, Mohammed Rahmatullah, Karma G. Dolma and Veeranoot Nissapatorn

F1000Res, 2023, 11, 1274
DOI: 10.12688/f1000research.126227.2

Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions

Haim Yuval Aviram, Menahem Pirchi, Hisham Mazal, Yoav Barak, Inbal Riven and Gilad Haran

Proc. Natl. Acad. Sci. U.S.A., 2018, 115, 3243
DOI: 10.1073/pnas.1720448115

The anticancer and anti-inflammatory activity screening of pyridazinone-based analogs against human epidermoid skin cancer with detailed mechanistic analyses

Rana Bershawy, Hani S. Hafez, Sahar S. El-Sakka, Ali Hammad and Mohammed H. Soliman

Journal of Biomolecular Structure and Dynamics, 2024, 42, 12885
DOI: 10.1080/07391102.2023.2273985

Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine

Hisham Mazal, Marija Iljina, Yoav Barak, Nadav Elad, Rina Rosenzweig, Pierre Goloubinoff, Inbal Riven and Gilad Haran

Nat Commun, 2019, 10
DOI: 10.1038/s41467-019-09474-6

Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold

Mona Gupta, Ravindra Venkatramani and Sri Rama Koti Ainavarapu

J. Phys. Chem. B, 2021, 125, 1009
DOI: 10.1021/acs.jpcb.0c08085

Capillary electrophoresis for enzyme-based studies: Applications to lipases and kinases

Ghassan Al Hamoui Dit Banni and Reine Nehmé

Journal of Chromatography A, 2022, 1661, 462687
DOI: 10.1016/j.chroma.2021.462687

Discovery of triaromatic flexible agents bearing 1,2,3-Triazole with selective and potent anti-breast cancer activity and CDK9 inhibition supported by molecular dynamics

Saleh K. Ihmaid, Ateyatallah Aljuhani, Mosa Alsehli, Nadjet Rezki, Ali Alawi, Ahmed J. Aldhafiri, Samir A. Salama, Hany E.A. Ahmed and Mohamed R. Aouad

Journal of Molecular Structure, 2022, 1249, 131568
DOI: 10.1016/j.molstruc.2021.131568

Ellagic Acid Modulates Uninduced as well as Mutation and Metal-Induced Aggregation of α-Synuclein: Implications for Parkinson’s Disease

Vinod Kumar Meena, Vijay Kumar, Shivani Karalia, Garima and Monica Sundd

ACS Chem. Neurosci., 2021, 12, 3598
DOI: 10.1021/acschemneuro.1c00317

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Eitan Lerner, Anders Barth, Jelle Hendrix, Benjamin Ambrose, Victoria Birkedal, Scott C Blanchard, Richard Börner, Hoi Sung Chung, Thorben Cordes, Timothy D Craggs, Ashok A Deniz, Jiajie Diao, Jingyi Fei, Ruben L Gonzalez, Irina V Gopich, Taekjip Ha, Christian A Hanke, Gilad Haran, Nikos S Hatzakis, Sungchul Hohng, Seok-Cheol Hong, Thorsten Hugel, Antonino Ingargiola, Chirlmin Joo, Achillefs N Kapanidis, Harold D Kim, Ted Laurence, Nam Ki Lee, Tae-Hee Lee, Edward A Lemke, Emmanuel Margeat, Jens Michaelis, Xavier Michalet, Sua Myong, Daniel Nettels, Thomas-Otavio Peulen, Evelyn Ploetz, Yair Razvag, Nicole C Robb, Benjamin Schuler, Hamid Soleimaninejad, Chun Tang, Reza Vafabakhsh, Don C Lamb, Claus AM Seidel and Shimon Weiss

eLife, 2021, 10
DOI: 10.7554/eLife.60416

Conjugated Dienones from Differently Substituted Cinnamaldehyde as Highly Potent Monoamine Oxidase-B Inhibitors: Synthesis, Biochemistry, and Computational Chemistry

Bijo Mathew, Jong Min Oh, Mohamed A. Abdelgawad, Ahmed Khames, Mohammed M. Ghoneim, Sunil Kumar, Lekshmi R. Nath, Sachithra Thazhathuveedu Sudevan, Della Grace Thomas Parambi, Clement Agoni, Mahmoud E. S. Soliman and Hoon Kim

ACS Omega, 2022, 7, 8184
DOI: 10.1021/acsomega.2c00397

Molecular Docking and Molecular Dynamics Aided Virtual Search of OliveNet™ Directory for Secoiridoids to Combat SARS-CoV-2 Infection and Associated Hyperinflammatory Responses

Neelaveni Thangavel, Mohammad Al Bratty, Hassan Ahmad Al Hazmi, Asim Najmi and Reem Othman Ali Alaqi

Front. Mol. Biosci., 2021, 7
DOI: 10.3389/fmolb.2020.627767

Molecular docking and MD simulations predicted quercetin as a potent human interleukin-1 beta (hIL1β) inhibitor for improved endodontic disease management

Nezar Boreak, Shroog Ali Almasoudi, Abdulelah Alharbi, Mona Judayba, Shahd Tahrei, Atyaf Abu eishah, Taghreed Ahmed Madkhali, Mashael Ali Hattan, Maryam Hassan Majrashi, Huda Ali Daak, Amani Hakami and Jorddy Neves Cruz

PLoS One, 2025, 20, e0336841
DOI: 10.1371/journal.pone.0336841

The anticancer and EGFR-TK/CDK-9 dual inhibitory potentials of new synthetic pyranopyrazole and pyrazolone derivatives: X-ray crystallography, in vitro , and in silico mechanistic investigations

Arafa Musa, Saleh K. Ihmaid, David L. Hughes, Musa A. Said, Hamada S. Abulkhair, Ahmed H. El-Ghorab, Mohamed A. Abdelgawad, Khaled Shalaby, Mohamed E. Shaker, Khalid Saad Alharbi, Nasser Hadal Alotaibi, Deborah L. Kays, Laurence J. Taylor, Della Grace Thomas Parambi, Sami I. Alzarea, Ahmed A. Al-Karmalawy, Hany E. A. Ahmed and Ahmed M. El-Agrody

Journal of Biomolecular Structure and Dynamics, 2023, 41, 12411
DOI: 10.1080/07391102.2023.2167000

Conformational constraints and ligand interactions are key determinants of the distinct aggregation pathways observed in human serum albumin

Chanchal Chauhan, Kehkashan Naaz, Shivani A. Muthu, Suhel Parvez and Basir Ahmad

International Journal of Biological Macromolecules, 2025, 334, 148952
DOI: 10.1016/j.ijbiomac.2025.148952

Lectin-carbohydrate analysis by molecular dynamics: Parkia lectins case study

KYRIA S. NASCIMENTO, VINICIUS J.S. OSTERNE, MESSIAS V. OLIVEIRA, JORGE L.C. DOMINGOS, WANDEMBERG P. FERREIRA, ELS J.M. VAN DAMME, BENILDO S. CAVADA and VANIR R. PINTO-JUNIOR

An. Acad. Bras. Ciênc., 2024, 96
DOI: 10.1590/0001-3765202420230677

From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

Dominika Gruszka, Pétur O. Heidarsson and Ciro Cecconi

Essays in Biochemistry, 2021, 65, 129
DOI: 10.1042/EBC20200024

Single‐Molecule FRET of Membrane Transport Proteins

Kim Bartels, Tanya Lasitza‐Male, Hagen Hofmann and Christian Löw

ChemBioChem, 2021, 22, 2657
DOI: 10.1002/cbic.202100106

Mechanistic insights into monomer level prevention of amyloid aggregation of lysozyme by glycyrrhizic acid

Shivani A. Muthu, Rahul Sharma, Afnaan Qureshi, Suhel Parvez and Basir Ahmad

International Journal of Biological Macromolecules, 2023, 227, 884
DOI: 10.1016/j.ijbiomac.2022.12.166

Entropic Inhibition: How the Activity of a AAA+ Machine Is Modulated by Its Substrate-Binding Domain

Marija Iljina, Hisham Mazal, Pierre Goloubinoff, Inbal Riven and Gilad Haran

ACS Chem. Biol., 2021, 16, 775
DOI: 10.1021/acschembio.1c00156