Works matching DE "PROTEIN-ligand interactions"

Results: 1263

Solvation and formal charge corrections to the Piecewise-Linear Potential.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00608-1

By:

Gehlhaar, Daniel K.;
Mermelstein, Daniel J.

Publication type:

Article

KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through in silico analysis.

Published in:

PLoS ONE, 2025, v. 20, n. 6, p. 1, doi. 10.1371/journal.pone.0324678

By:

Azmi, Muhammad Bilal;
Kumari, Simran;
Aquil, Sakina;
Nizami, Urooj;
Sohail, Arisha;
Ahmed, Syed Danish Haseen;
Qureshi, Shamim Akhtar

Publication type:

Article

Extracellular ligand-responsive translational regulation of synthetic mRNAs using engineered receptors.

Published in:

NPG Asia Materials, 2025, v. 17, n. 1, p. 1, doi. 10.1038/s41427-025-00607-6

By:

Nakanishi, Hideyuki;
Itaka, Keiji

Publication type:

Article

Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies.

Published in:

Amino Acids, 2025, v. 57, n. 1, p. 1, doi. 10.1007/s00726-025-03457-2

By:

Ahmed, Shazia;
Choudhury, Arunabh;
Saeed, Mohammad Umar;
Mohammad, Taj;
Hussain, Afzal;
Alajmi, Mohamed F.;
Yadav, Dharmendra Kumar;
Shamsi, Anas;
Hassan, Md. Imtaiyaz

Publication type:

Article

Identification of CD36 as a contributor in inflammatory response of rheumatoid arthritis and screening of feasible bioactive drugs targeting it.

Published in:

Hereditas, 2025, v. 162, n. 1, p. 1, doi. 10.1186/s41065-025-00450-3

By:

Xuan, Dan;
Wang, Xiaowan;
Feng, Dandan;
Wang, Li;
Xia, Yonghui

Publication type:

Article

Strategic Identification of Anti-Cancer Compounds Targeting PARP15 in DNA Repair Pathways for Enhanced Therapeutic Efficacy.

Published in:

Polycyclic Aromatic Compounds, 2025, v. 45, n. 4, p. 580, doi. 10.1080/10406638.2024.2413032

By:

Sharma, Pradeep;
Sharma, Sujata;
Alam, Aftab;
Alqarni, Mohammed H.;
Bhardwaj, Rima;
Singh, Indrakant K.

Publication type:

Article

Author Index Volume 24 (2025).

Published in:: Journal of Computational Biophysics & Chemistry, 2025, v. 24, n. 10, p. 1457, doi. 10.1142/S2737416525990017
Publication type:: Article

15th EBSA congress, June 30 – July 4, 2025, Rome, Italy – Abstracts.

Published in:: 2025
Publication type:: Calendar

Discovery, Biological Evaluation and Binding Mode Investigation of Novel Butyrylcholinesterase Inhibitors Through Hybrid Virtual Screening.

Published in:

Molecules, 2025, v. 30, n. 10, p. 2093, doi. 10.3390/molecules30102093

By:

Li, Lizi;
Zhao, Puchen;
Yang, Can;
Yin, Qin;
Wang, Na;
Liu, Yan;
Li, Yanfang

Publication type:

Article

Discovery of Lithospermate B as a Potential Ligand for the Malarial E2 Ubiquitin-Conjugating Enzyme via Multiplexed Native Mass Spectrometry.

Published in:

Chemosensors, 2025, v. 14, n. 5, p. 166, doi. 10.3390/chemosensors13050166

By:

Han, Jianying;
Van Voorhis, Wesley C.;
Quinn, Ronald J.;
Liu, Miaomiao

Publication type:

Article

Advanced modeling of salt-inducible kinase (SIK) inhibitors incorporating protein flexibility through molecular dynamics and cross-docking.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-03699-w

By:

Valdés-Albuernes, Jorge Luis;
Díaz-Pico, Erbio;
Alfaro, Sergio;
Caballero, Julio

Publication type:

Article

Evaluating the Antiviral Potential of Polyherbal Formulation (Kabasura Kudineer) Against Monkeypox Virus: Targeting E5, Poxin, and DNA Polymerase Through Multifaceted Drug Discovery Approaches.

Published in:

Life (2075-1729), 2025, v. 15, n. 5, p. 771, doi. 10.3390/life15050771

By:

Priya, Sivan Padma;
Amalraj, Singamoorthy;
Padmanabhan, Vivek;
Rahman, Mohammed Mustahsen;
Chaitanya, Nallan CSK;
Hashim, Nada Tawfig;
Prabhu, Srinivasan;
Ayyanar, Muniappan;
Gurav, Shailendra;
Ceasar, Stanislaus Antony;
Thiruvengadam, Rekha

Publication type:

Article

Structural Insights into Benzothiazole Derivatives as Modulators of Dehaloperoxidase: A Docking Study.

Published in:

Bulletin of Pure & Applied Sciences-Chemistry, 2024, v. 43, n. 2, p. 69

By:

Sur, Souvik

Publication type:

Article

Green Synthesis of Nanoscale Mixed‐Ligand Complexes: DNA Interaction, Biomedical Applications, and Computational Studies.

Published in:

Applied Organometallic Chemistry, 2025, v. 39, n. 6, p. 1, doi. 10.1002/aoc.70230

By:

Hosny, Shimaa;
Abu‐Dief, Ahmed M.;
Farhan, Nasser;
Shehata, Mohamed R.;
Abd El‐Baki, Randa F.

Publication type:

Article

In Silico Identification of 2,4-Diaminopyrimidine-Based Compounds as Potential CK1ε Inhibitors.

Published in:

Pharmaceuticals (14248247), 2025, v. 18, n. 5, p. 741, doi. 10.3390/ph18050741

By:

Sánchez-Álvarez, Axel A.;
Velasco-Velázquez, Marco A.;
Cordova-Bahena, Luis

Publication type:

Article

Identification of Bacterial Oligopeptidase B Inhibitors from Microbial Natural Products: Molecular Insights, Docking Studies, MD Simulations, and ADMET Predictions.

Published in:

Pharmaceuticals (14248247), 2025, v. 18, n. 5, p. 709, doi. 10.3390/ph18050709

By:

Mohamed, Malik Suliman;
Elsaman, Tilal;
Mohamed, Magdi Awadalla;
Eltayib, Eyman Mohamed;
Abdalla, Abualgasim Elgaili;
Idriss, Mona Timan

Publication type:

Article

Virtual Screening and Molecular Dynamics Simulation Targeting the ATP Domain of African Swine Fever Virus Type II DNA Topoisomerase.

Published in:

Viruses (1999-4915), 2025, v. 17, n. 5, p. 681, doi. 10.3390/v17050681

By:

Zhao, Rui;
Hou, Lezi;
Tesfagaber, Weldu;
Song, Linfei;
Zhang, Zhenjiang;
Li, Fang;
Bu, Zhigao;
Zhao, Dongming

Publication type:

Article

In silico Prediction of Molecular Docking between Chicken BRD2 and Newcastle Disease Virus Matrix Protein to Elucidate Host-pathogen Interactio.

Published in:

Agricultural Science Digest, 2025, v. 45, n. 2, p. 337, doi. 10.18805/ag.D-5508

By:

Singh, Paramvir;
Mukhopadhyay, C. S.;
Dash, Shakti Kant

Publication type:

Article

Nephron progenitor fate is modulated by angiotensin type 1 receptor signaling in human kidney organoids Open Access.

Published in:

Stem Cells, 2025, v. 43, n. 5, p. 1, doi. 10.1093/stmcls/sxaf012

By:

Chung, Hyunjae;
Rahmani, Waleed;
Sinha, Sarthak;
Imanzadeh, Aysa;
Pun, Alexander;
Arora, Rohit;
Jaffer, Arzina;
Biernaskie, Jeff;
Chun, Justin

Publication type:

Article

Kisspeptin Receptor Agonists and Antagonists: Strategies for Discovery and Implications for Human Health and Disease.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4890, doi. 10.3390/ijms26104890

By:

Chen, Xing;
Yang, Shu;
Shaw, Natalie D.;
Xia, Menghang

Publication type:

Article

Apoptosis and G2/M Phase Cell Cycle Arrest Induced by Alkaloid Erythraline Isolated from Erythrina velutina in SiHa Cervical Cancer Cell.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4627, doi. 10.3390/ijms26104627

By:

Miranda, Cleine Aglacy Nunes;
Souza, Amaxsell Thiago Barros de;
Soares, Ana Katarina Menezes da Cruz;
Bernardes-Oliveira, Emanuelly;
Rocha, Hugo Alexandre Oliveira;
Barbosa, Euzébio Guimarães;
Guaratini, Thais;
Lucena-Silva, Norma;
Cobucci, Ricardo Ney;
Giordani, Raquel Brandt;
Crispim, Janaina Cristiana de Oliveira

Publication type:

Article

In Silico Approach to Design of New Multi-Targeted Inhibitors Based on Quinoline Ring with Potential Anticancer Properties.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4620, doi. 10.3390/ijms26104620

By:

Czyżnikowska, Żaneta;
Mysłek, Martyna;
Marciniak, Aleksandra;
Płaczek, Remigiusz;
Kotynia, Aleksandra;
Krzyżak, Edward

Publication type:

Article

Special Issue: Discovery of Bioactive Phytochemicals' Molecular Mechanisms Against Different Diseases Based on Network Pharmacology and Molecular Docking.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 10, p. 4516, doi. 10.3390/ijms26104516

By:

Xu, Baojun

Publication type:

Article

Synthesis, characterization, biological evaluation and molecular docking of a Schiff base ligand and its metal complexes.

Published in:

BioMetals, 2025, v. 38, n. 3, p. 935, doi. 10.1007/s10534-025-00688-4

By:

AbouElleef, Elsayed M.;
Saad, Rania A.;
Diab, M. A.;
El-Zahed, M. M.;
El-Sonbati, A. Z.;
Morgan, Sh. M.

Publication type:

Article

StructureNet: Physics-Informed Hybridized Deep Learning Framework for Protein–Ligand Binding Affinity Prediction.

Published in:

Bioengineering (Basel), 2025, v. 12, n. 5, p. 505, doi. 10.3390/bioengineering12050505

By:

Kaneriya, Arjun;
Samudrala, Madhav;
Ganesh, Harrish;
Moran, James;
Dandibhotla, Somanath;
Dakshanamurthy, Sivanesan

Publication type:

Article

Machine Learning-Based Virtual Screening and Molecular Modeling Reveal Potential Natural Inhibitors for Non-Small Cell Lung Cancer.

Published in:

Crystals (2073-4352), 2025, v. 15, n. 5, p. 383, doi. 10.3390/cryst15050383

By:

Al Shehri, Zafer Saad;
Alshehri, Faez Falah

Publication type:

Article

Notch signaling pathway in cumulus cells can be a novel marker to identify poor and normal responder IVF patients.

Published in:

Journal of Assisted Reproduction & Genetics, 2013, v. 30, n. 10, p. 1319, doi. 10.1007/s10815-013-0072-4

By:

Tanriverdi, Gamze;
Denir, Secnur;
Ayla, Sule;
Bilir, Ayhan;
Oktar, Huseyin;
Cepni, Ismail;
Irez, Tulay

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

Molecular Recognition of Natural and Non‐Natural Substrates by Cellodextrin Phosphorylase from Ruminiclostridium Thermocellum Investigated by NMR Spectroscopy.

Published in:

Chemistry - A European Journal, 2021, v. 27, n. 63, p. 15688, doi. 10.1002/chem.202102039

By:

Gabrielli, Valeria;
Muñoz‐García, Juan C.;
Pergolizzi, Giulia;
de Andrade, Peterson;
Khimyak, Yaroslav Z.;
Field, Robert A.;
Angulo, Jesús

Publication type:

Article

In Cellulo Generation of Fluorescent Probes for Live‐Cell Imaging of Cylooxygenase‐2.

Published in:

Chemistry - A European Journal, 2021, v. 27, n. 10, p. 3326, doi. 10.1002/chem.202003315

By:

Kaur, Jatinder;
Bhardwaj, Atul;
Wuest, Frank

Publication type:

Article

Exploring Multi‐Subsite Binding Pockets in Proteins: DEEP‐STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B.

Published in:

Chemistry - A European Journal, 2020, v. 26, n. 44, p. 10024, doi. 10.1002/chem.202001723

By:

Monaco, Serena;
Walpole, Samuel;
Doukani, Hassan;
Nepravishta, Ridvan;
Martínez‐Bailén, Macarena;
Carmona, Ana T.;
Ramos‐Soriano, Javier;
Bergström, Maria;
Robina, Inmaculada;
Angulo, Jesus

Publication type:

Article

A Coumarin Triflate Reagent Enables One‐Step Synthesis of Photo‐Caged Lipid Metabolites for Studying Cell Signaling.

Published in:

Chemistry - A European Journal, 2019, v. 25, n. 68, p. 15483, doi. 10.1002/chem.201903909

By:

Wagner, Nicolai;
Schuhmacher, Milena;
Lohmann, Annett;
Nadler, André

Publication type:

Article

Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR.

Published in:

Angewandte Chemie, 2016, v. 128, n. 38, p. 11710, doi. 10.1002/ange.201606335

By:

Joseph, Benesh;
Tormyshev, Victor M.;
Rogozhnikova, Olga Yu.;
Akhmetzyanov, Dmitry;
Bagryanskaya, Elena G.;
Prisner, Thomas F.

Publication type:

Article

Accelerating the Association of the Most Stable Protein-Ligand Complex by More than Two Orders of Magnitude.

Published in:

Angewandte Chemie, 2016, v. 128, n. 32, p. 9496, doi. 10.1002/ange.201603652

By:

Giese, Christoph;
Eras, Jonathan;
Kern, Anne;
Schärer, Martin A.;
Capitani, Guido;
Glockshuber, Rudi

Publication type:

Article

Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein-Ligand Interactions.

Published in:

Angewandte Chemie, 2016, v. 128, n. 15, p. 4816, doi. 10.1002/ange.201600593

By:

Guo, Yuan;
Sakonsinsiri, Chadamas;
Nehlmeier, Inga;
Fascione, Martin A.;
Zhang, Haiyan;
Wang, Weili;
Pöhlmann, Stefan;
Turnbull, W. Bruce;
Zhou, Dejian

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

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions.

Published in:

Journal of Biological Physics, 2014, v. 40, n. 2, p. 121, doi. 10.1007/s10867-014-9341-4

By:

Woods, K.

Publication type:

Article

Structural evidences for a secondary gold binding site in the hydrophobic box of lysozyme.

Published in:

BioMetals, 2015, v. 28, n. 4, p. 745, doi. 10.1007/s10534-015-9863-7

By:

Ferraro, Giarita;
Massai, Lara;
Messori, Luigi;
Cinellu, Maria;
Merlino, Antonello

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

Ligandbook: an online repository for small and drug-like molecule force field parameters.

Published in:

Bioinformatics, 2017, v. 33, n. 11, p. 1747, doi. 10.1093/bioinformatics/btx037

By:

Domański, Jan;
Beckstein, Oliver;
Iorga, Bogdan I.

Publication type:

Article

SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.

Published in:

Bioinformatics, 2017, v. 33, n. 8, p. 1238, doi. 10.1093/bioinformatics/btw829

By:

Litfin, Thomas;
Yaoqi Zhou;
Yuedong Yang

Publication type:

Article

ModuleAlign: module-based global alignment of protein-protein interaction networks.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i658, doi. 10.1093/bioinformatics/btw447

By:

Hashemifar, Somaye;
Jianzhu Ma;
Naveed, Hammad;
Canzar, Stefan;
Jinbo Xu

Publication type:

Article

Alloscore: a method for predicting allosteric ligand--protein interactions.

Published in:

Bioinformatics, 2016, v. 32, n. 10, p. 1574, doi. 10.1093/bioinformatics/btw036

By:

Shuai Li;
Qiancheng Shen;
Minyi Su;
Xinyi Liu;
Shaoyong Lu;
Zhongjie Chen;
Renxiao Wang;
Jian Zhang

Publication type:

Article

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 901, doi. 10.1093/bioinformatics/btv593

By:

Yusuke Komiyama;
Masaki Banno;
Kokoro Ueki;
Saad, Gul;
Kentaro Shimizu

Publication type:

Article

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.

Published in:

Bioinformatics, 2015, v. 31, n. 23, p. 3856, doi. 10.1093/bioinformatics/btv458

By:

Gaudreault, Francis;
Morency, Louis-Philippe;
Najmanovich, Rafael J.

Publication type:

Article

The anisotropic network model web server at 2015 (ANM 2.0).

Published in:

2015

By:

Eyal, Eran;
Lum, Gengkon;
Bahar, Ivet

Publication type:

Product Review

Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. 1674, doi. 10.1093/bioinformatics/btu104

By:

Cao, Yang;
Li, Lei

Publication type:

Article

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1314, doi. 10.1093/bioinformatics/btu002

By:

Panjkovich, Alejandro;
Daura, Xavier

Publication type:

Article