Works about PROTEIN-ligand interactions

Results: 1219

Phytochemical compounds against mild cognitive impairment key proteins: An in-silico approach.

Published in:

Journal of Applied Pharmaceutical Science, 2025, v. 15, n. 5, p. 090, doi. 10.7324/JAPS.2025.209505

By:

Gonzalez-Ruiz, Cristian;
Hidalgo, Isabel;
Portilla-Martínez, Andrés;
Rubio-Gayosso, Iván;
Salgado-Ceballos, Hermelinda;
Fabela-Sánchez, Omar;
Bernal-Hernández, Jorge;
Ortiz-Flores, Miguel

Publication type:

Article

Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-59930-9

By:

Troester, Selina;
Eder, Thomas;
Wukowits, Nadja;
Piontek, Martin;
Fernández-Pernas, Pablo;
Schmoellerl, Johannes;
Haladik, Ben;
Manhart, Gabriele;
Allram, Melanie;
Maurer-Granofszky, Margarita;
Scheidegger, Nastassja;
Nebral, Karin;
Superti-Furga, Giulio;
Meisel, Roland;
Bornhauser, Beat;
Valent, Peter;
Dworzak, Michael N.;
Zuber, Johannes;
Boztug, Kaan;
Grebien, Florian

Publication type:

Article

Computational drug repurposing reveals potential alanine racemase inhibitors for combating drug-resistant tuberculosis.

Published in:

Biologia, 2025, v. 80, n. 6, p. 1513, doi. 10.1007/s11756-025-01916-5

By:

LakshmanaPerumal, Keerthika;
Vetrivel, Umashankar

Publication type:

Article

Assessing interaction recovery of predicted protein-ligand poses.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01011-6

By:

Errington, David;
Schneider, Constantin;
Bouysset, Cédric;
Dreyer, Frédéric A.

Publication type:

Article

Discovery of Galangin Derivatives as a Potential T-cell Leukemia Virus 1 Protease Inhibitor Through Chemoinformatics Approaches.

Published in:

Cell Biochemistry & Biophysics, 2025, v. 83, n. 2, p. 2067, doi. 10.1007/s12013-024-01618-w

By:

Akash, Shopnil;
Sultana, Sharifa;
Islam, Mirza Nafeul;
Or Rashid, Md. Harun;
Oduselu, Gbolahan Oladipupo;
Kaouche, Farah Chafika;
Sindi, Emad Rashad;
de Farias Morais, Gabriel Christian;
Al-Dies, Al-Anood M.;
Oliveira, Jonas Ivan Nobre

Publication type:

Article

Targeting multiple pathways with virtual screening to identify the multi-target agent for Alzheimer's disease treatment.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00602-7

By:

Takomthong, Pitchayakarn;
Waiwut, Pornthip;
Boonyarat, Chantana

Publication type:

Article

Understanding the Molecular Landscape of Endometriosis: A Bioinformatics Approach to Uncover Signaling Pathways and Hub Genes.

Published in:

IJ Pharmaceutical Research (IJPR), 2024, v. 23, n. 1, p. 1, doi. 10.5812/ijpr-144266

By:

Tian, Junhua;
Liu, Xiaochun

Publication type:

Article

Dipeptidyl Peptidase-4 Inhibitors: A Systematic Review of Structure-Activity Relationship Studies.

Published in:

IJ Pharmaceutical Research (IJPR), 2024, v. 23, n. 1, p. 1, doi. 10.5812/ijpr-151581

By:

Bayanati, Maryam;
Rabbani, Mohammad Ismail Mahboubi;
Kabiri, Shirin Sirous;
Mir, Bahareh;
Rezaee, Elham;
Tabatabai, Sayyed Abbas

Publication type:

Article

Pericytes: The forgotten controllers of a functional blood–brain barrier.

Published in:

PLoS Pathogens, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.ppat.1013145

By:

Roedel, Marshall;
Brooks, Nia;
Lamb, Tracey J.

Publication type:

Article

Inhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca<sup>2+</sup> dependent allosteric binding site.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-59919-4

By:

Dakin, Leslie A.;
Xing, Li;
Hall, Justin;
Ding, Weidong;
Vajdos, Felix F.;
Pelker, Jeffrey W.;
Ramsey, Simeon;
Balbo, Paul;
Sahasrabudhe, Parag V.;
Banker, Mary Ellen;
Choi, Won Young;
Wright, Stephen W.;
Chang, Jeanne S.;
Curto, John M.;
Davoren, Jennifer E.;
Drozda, Susan E.;
Fennell, Kimberly F.;
Futatsugi, Kentaro;
Kortum, Steve;
Lee, Katherine L.

Publication type:

Article

Fast and flu-rious: How to prevent and treat emerging influenza A viruses.

Published in:

PLoS Pathogens, 2025, v. 21, n. 5, p. 1, doi. 10.1371/journal.ppat.1013135

By:

Sesifredo, Isabel;
Batalha, Íris Luz;
Amorim, Maria João

Publication type:

Article

Computational investigation of natural compounds as inhibitors against macrolide-resistant protein using virtual screening, molecular docking and MD simulations.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-97083-3

By:

Alanzi, Abdullah R.;
Alhaidhal, Bayan Abdullah;
Aloatibi, Raghad Mohammad

Publication type:

Article

Harnessing Spirulina Extract to Enhance Drought Tolerance in Wheat: A Morphological, Molecular Genetic and Molecular Docking Approach.

Published in:

Egyptian Academic Journal of Biological Sciences, H. Botany, 2024, v. 15, n. 2, p. 73, doi. 10.21608/EAJBSH.2024.397935

By:

Ibrahim, Mona I. M.;
Ahmed, Alshimaa T.;
El-Dougdoug, Khaled A.;
El Nady, Ghada H.

Publication type:

Article

Cholesterol Concentration in Cell Membranes and its Impact on Receptor–Ligand Interaction: A Computational Study of ATP-Sensitive Potassium Channels and ATP Binding.

Published in:

Journal of Membrane Biology, 2025, v. 258, n. 3, p. 225, doi. 10.1007/s00232-025-00345-4

By:

Millan-Pacheco, Cesar;
Serratos, Iris N.;
Félix-Martínez, Gerardo J.;
Blancas-Flores, Gerardo;
Osorno, Alejandra;
Godínez, Rafael

Publication type:

Article

The Licochalcone Compound A: Theoretical Studies Applied with DFT Method and Molecular Docking Simulations.

Published in:

Journal of Natural & Applied Sciences, 2025, v. 29, n. 1, p. 12, doi. 10.19113/sdufenbed.1560727

By:

KARTAL, Barış;
TANRIVERDİ, Aslıhan Aycan;
YILDIKO, Ümit

Publication type:

Article

Allosteric modulation of Plasmodium falciparum Isoleucyl tRNA synthetase by South African natural compounds.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0321444

By:

Chepsiror, Curtis;
Veldman, Wayde;
Olotu, Fisayo;
Tastan Bishop, Özlem

Publication type:

Article

Structural insights into ligand recognition and activation of human purinergic receptor P2Y14.

Published in:

Cell Discovery, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41421-025-00799-9

By:

Gu, Quanchang;
Lv, Zhenyu;
Wang, Tianxin;
Tang, Wenqin;
Guo, Xuzhen;
Huang, Xiangling;
Li, Fahui;
Wang, Jiangyun

Publication type:

Article

Discovery of ROCK2 inhibitors through computational screening of ZINC database: Integrating pharmacophore modeling, molecular docking, and MD simulations.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0323781

By:

Alanzi, Abdullah R.;
Shahat, Abdelaaty A.;
Alhaidhal, Bayan Abdullah;
Aloatibi, Raghad Mohammad

Publication type:

Article

PSGL-1: A Universal Selectin Ligand or a Signaling Molecule? (Review of the Literature).

Published in:

Molecular Biology, 2025, v. 59, n. 1, p. 26, doi. 10.1134/S0026893324700699

By:

Korotkova, N. V.;
Kalinin, R. E.;
Suchkov, I. A.;
Mzhavanadze, N. D.;
Nikiforova, L. V.

Publication type:

Article

Viral fusion proteins of classes II and III recognize and reorganize complex biological membranes.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08040-9

By:

Poojari, Chetan S.;
Bommer, Tobias;
Hub, Jochen S.

Publication type:

Article

DETERMINATION OF ALPHA GLUCOSIDASE INHIBITION ACTIVITY OF ODINA WODIER BARK.

Published in:

Obstetrics & Gynaecology Forum, 2024, v. 34, n. 2, p. 623

By:

p., Abisha;
Arthanari, Abirami;
Sankar, Sathish

Publication type:

Article

GC-MS Analysis, Molecular Docking, Dynamics and ADMET Profiling of Algerian Origanum vulgare Essential Oil Compounds as Potential COVID-19 Inhibitors.

Published in:

Journal of Computational Biophysics & Chemistry, 2025, v. 24, n. 8, p. 1009, doi. 10.1142/S2737416525500073

By:

Mouada, Hanane;
Stiti, Mohamed Zakaria;
Zafar, Imran;
Boutarfaia, Amira;
Djellaili, Lamia;
Berregouba, Fatma Lylia;
Aissani, Sana

Publication type:

Article

Computational investigation of natural compounds as inhibitors against macrolide-resistant protein using virtual screening, molecular docking and MD simulations.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-97083-3

By:

Alanzi, Abdullah R.;
Alhaidhal, Bayan Abdullah;
Aloatibi, Raghad Mohammad

Publication type:

Article

In silico approach for uncovering inhibitors of SARS-CoV-2 by targeting TMPRSS2 via molecular networking-based strategies.

Published in:

Indian Journal of Biochemistry & Biophysics, 2025, v. 62, n. 5, p. 544, doi. 10.56042/ijbb.v62i5.4034

By:

Parameswaran, Dakshinesh;
Thangavelu, Saravanan;
Jubie, Selvaraj;
Swaroop, Akey Krishna;
Chellappa, Selvinthanuja;
Vivekanandan, Lalitha;
Thangavel, Sivakumar;
Thangavelu, Prabha

Publication type:

Article

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD).

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.96513

By:

Deganutti, Giuseppe;
Pipito, Ludovico;
Rujan, Roxana Maria;
Weizmann, Tal;
Griffin, Peter;
Ciancetta, Antonella;
Moro, Stefano;
Reynolds, Christopher Arthur

Publication type:

Article

Unveiling Protein-Ligand Interactions: Regression Methods for Binding Affinity Prediction.

Published in:

International Journal on Engineering Applications, 2024, v. 12, n. 6, p. 508, doi. 10.15866/irea.v12i6.25407

By:

Gök, Murat;
Cengiz, Emine;
Mijwil, Maad M.

Publication type:

Article

Structural Insights and Drug Repurposing of FDA-Approved Molecules against Human Agmatinase in Cancer Therapy.

Published in:

Journal of Computational Biophysics & Chemistry, 2025, v. 24, n. 6, p. 767, doi. 10.1142/S2737416524500820

By:

Khan, Zeeshan;
Ikram, Saima;
Ahmad, Jamshaid;
Ur Rehman, Irshad;
Ahsan, Hina;
Ullah, Amin;
Alshaya, Dalal Sulaiman;
Fayad, Eman;
Hassan, Hesham M.;
Eldeen, Muhammad Alaa

Publication type:

Article

Screening the Pandemic Response Box identifies novel ligands of the Staphylococcus aureus protein arginine kinase, McsB.

Published in:

Molecular Biology Reports, 2025, v. 52, n. 1, p. 1, doi. 10.1007/s11033-025-10545-9

By:

Chetty, Ryan;
Delport, Alexandré;
Mthembu, Sandile;
Veale, Clinton G. L.;
Hewer, Raymond

Publication type:

Article

Exploring bioactive phytoconstituents as USP21 inhibitors for therapeutic development against cancer.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-94825-1

By:

Anwar, Saleha;
Khan, Mohd Shahnawaz;
Yadav, Dharmendra Kumar;
Shahwan, Moyad;
Shamsi, Anas

Publication type:

Article

Predicting inhibitors of OATP1B1 via heterogeneous OATP-ligand interaction graph neural network (HOLIgraph).

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01020-5

By:

Mardikoraem, Mehrsa;
Eaves, Joelle N.;
Belecciu, Theodore;
Pascual, Nathaniel;
Aljets, Alexander;
Hagenbuch, Bruno;
Shapiro, Erik M.;
Orlando, Benjamin J.;
Woldring, Daniel R.

Publication type:

Article

Leveraging AI to explore structural contexts of post-translational modifications in drug binding.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01019-y

By:

Medvedev, Kirill E.;
Schaeffer, R. Dustin;
Grishin, Nick V.

Publication type:

Article

Structural insights into thraustochytrid-specific lipases using alphafold to identify the role of GXSXG motif.

Published in:

BMC Biotechnology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12896-025-00972-8

By:

Mariam, Iqra;
Rova, Ulrika;
Christakopoulos, Paul;
Matsakas, Leonidas;
Patel, Alok

Publication type:

Article

Virtual screening and molecular dynamics simulation study of ATP-competitive inhibitors targeting mTOR protein.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0319608

By:

Jin, Mei-Yu;
Yu, Hao;
Deng, Qiong;
Wang, Zhu;
Wang, Jie-Yan;
Li, Hao-Long;
Liang, Hui

Publication type:

Article

Structural insight into TLR4/MD-2 activation by synthetic LPS mimetics with distinct binding modes.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-59550-3

By:

Fu, Yaoyao;
Kim, Hyojin;
Lee, Dong Sun;
Han, Ah-reum;
Heine, Holger;
Zamyatina, Alla;
Kim, Ho Min

Publication type:

Article

Glycine-induced formation and druggability score prediction of protein surface pockets.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 5, p. N.PAG, doi. 10.1142/S0219720019500264

By:

Bongini, Pietro;
Niccolai, Neri;
Bianchini, Monica

Publication type:

Article

Boosted neural networks scoring functions for accurate ligand docking and ranking.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 2, p. -1, doi. 10.1142/S021972001850004X

By:

Ashtawy, Hossam M.;
Mahapatra, Nihar R.

Publication type:

Article

PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.

Published in:

Journal of Bioinformatics & Computational Biology, 2015, v. 13, n. 3, p. -1, doi. 10.1142/S0219720015410073

By:

Ng, Marcus C. K.;
Fong, Simon;
Siu, Shirley W. I.

Publication type:

Article

A REGIONALIZABLE STATISTICAL MODEL OF INTERSECTING REGIONS IN PROTEIN-LIGAND BINDING CAVITIES.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 3, p. 1242004-1, doi. 10.1142/S0219720012420048

By:

CHEN, BRIAN Y.;
BANDYOPADHYAY, SOUTIR

Publication type:

Article

CSCORE:: A SIMPLE YET EFFECTIVE SCORING FUNCTION FOR PROTEIN-LIGAND BINDING AFFINITY PREDICTION USING MODIFIED CMAC LEARNING ARCHITECTURE.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, p. 1, doi. 10.1142/S021972001100577X

By:

OUYANG, XUCHANG;
HANDOKO, STEPHANUS DANIEL;
KWOH, CHEE KEONG

Publication type:

Article

Detecting Protein‐Ligand Interactions with Nitroxide Based Paramagnetic Cosolutes.

Published in:

Chemistry - A European Journal, 2024, v. 30, n. 18, p. 1, doi. 10.1002/chem.202303570

By:

Penk, Anja;
Danielsson, Annemarie;
Gaardløs, Margrethe;
Montag, Cindy;
Schöler, Andrea;
Huster, Daniel;
Samsonov, Sergey A.;
Künze, Georg

Publication type:

Article

Alkyne Activation in the Diversity Oriented Synthesis of sp<sup>2</sup>‐Rich Scaffolds: A Biased Library Approach for Targeting Polynucleotides (DNA/RNA).

Published in:

Chemistry - A European Journal, 2022, v. 28, n. 71, p. 1, doi. 10.1002/chem.202201925

By:

Chen, Shuqi;
Priebbenow, Daniel L.;
Somkhit, Julie;
Scullino, Carmen V.;
Agama, Keli;
Pommier, Yves;
Flynn, Bernard L.

Publication type:

Article

Dissociation Kinetics of a Binary Complex in Solution by Protein Displacement.

Published in:

Angewandte Chemie, 2013, v. 125, n. 48, p. 12819, doi. 10.1002/ange.201306253

By:

Launay, Helene;
Parent, Benjamin;
Page, Adeline;
Hanoulle, Xavier;
Lippens, Guy

Publication type:

Article

Environment-Sensitive Fluorescent Turn-On Probes Targeting Hydrophobic Ligand-Binding Domains for Selective Protein Detection.

Published in:

Angewandte Chemie, 2013, v. 125, n. 31, p. 8282, doi. 10.1002/ange.201302884

By:

Zhuang, Yu ‐ De;
Chiang, Po ‐ Yi;
Wang, Chia ‐ Wen;
Tan, Kui ‐ Thong

Publication type:

Article

The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand.

Published in:

Angewandte Chemie, 2013, v. 125, n. 30, p. 7868, doi. 10.1002/ange.201301813

By:

Lockett, Matthew R.;
Lange, Heiko;
Breiten, Benjamin;
Heroux, Annie;
Sherman, Woody;
Rappoport, Dmitrij;
Yau, Patricia O.;
Snyder, Philip W.;
Whitesides, George M.

Publication type:

Article

Simultaneous Detection of Diverse Glycoligand-Receptor Recognitions Using a Single-Excitation, Dual-Emission Graphene Composite.

Published in:

Advanced Functional Materials, 2015, v. 25, n. 23, p. 3483, doi. 10.1002/adfm.201500448

By:

Ji, Ding‐Kun;
Chen, Guo‐Rong;
He, Xiao‐Peng;
Tian, He

Publication type:

Article

Correction to: Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions.

Published in:

2021

By:

Leherte, L.

Publication type:

Correction Notice

Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2021, v. 140, n. 1, p. 1, doi. 10.1007/s00214-020-02705-w

By:

Leherte, L.

Publication type:

Article

Non-canonical interactions of porphyrins in porphyrin-containing proteins.

Published in:

Amino Acids, 2012, v. 43, n. 4, p. 1535, doi. 10.1007/s00726-012-1228-8

By:

Stojanović, Srđan;
Isenović, Esma;
Zarić, Božidarka

Publication type:

Article

Investigation of Polyvinyl Alcohol (PVA)-Sakacin P Interaction by Molecular Docking Method.

Published in:

Istanbul Gelisim University Journal of Health Sciences / İstanbul Gelişim Üniversitesi Sağlık Bilimleri Dergisi, 2024, n. 22, p. 73, doi. 10.38079/igusabder.1224944

By:

ÜNLÜ, Nihan;
ÖZGEN, Arzu

Publication type:

Article

Regulation of the programmed cell death protein 1/programmed cell death ligand 1 axis in relapsing--remitting multiple sclerosis.

Published in:

Brain Communications, 2023, v. 5, n. 4, p. 1, doi. 10.1093/braincomms/fcad206

By:

Tsaktanis, Thanos;
Linnerbauer, Mathias;
Lößlein, Lena;
Farrenkopf, Daniel;
Vandrey, Oliver;
Peter, Anne;
Cirac, Ana;
Beyer, Tobias;
Nirschl, Lucy;
Grummel, Verena;
Mühlau, Mark;
Bussas, Matthias;
Hemmer, Bernhard;
Quintana, Francisco J.;
Rothhammer, Veit

Publication type:

Article