Works about PROTEIN-ligand interactions

Results: 1327

Cloning, heterologous expression, and expression analysis of SinSyn7 gene from Sinomenium acutum.

Published in:

PLoS ONE, 2025, v. 19, n. 7, p. 1, doi. 10.1371/journal.pone.0327959

By:

Chen, Jiabei;
Chen, Xinyu;
Zhang, Li;
Huang, Shiyi;
Chen, Xinbo;
Huang, Xueshuang;
Yang, Hua

Publication type:

Article

Computational insights into flavonoids inhibition of dengue virus envelope protein: ADMET profiling, molecular docking, dynamics, PCA, and end-state free energy calculations.

Published in:

PLoS ONE, 2025, v. 19, n. 7, p. 1, doi. 10.1371/journal.pone.0327862

By:

Waiba, Amar;
Phunyal, Anuraj;
Lamichhane, Tika Ram;
Ghimire, Madhav Prasad;
Nyaupane, Hari;
Phuyal, Ashish;
Adhikari, Achyut

Publication type:

Article

Chemoproteomics identifies protein ligands for monoacylglycerol lipids.

Published in:

Communications Chemistry, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42004-025-01589-w

By:

Shanbhag, Karthik;
Mhetre, Amol B.;
Saharan, Ojal;
Devarajan, Archit;
Rai, Anisha;
Madhusudhan, M. S.;
Chakrapani, Harinath;
Kamat, Siddhesh S.

Publication type:

Article

Identification of Phytochemicals as Promising GSK-3β Inhibitors for Cancer Therapeutic Potential Through Virtual Screening, Molecular Docking, MD Simulation and MM-PBSA Calculation.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 3, p. 485, doi. 10.1142/S2737416525500565

By:

Saadh, Mohamed J.;
Hussein, Wael Sheet;
Alfarttoosi, Karar H.;
Bishoyi, Ashok Kumar;
Roopashree, R.;
Kundlas, Mayank;
Chennakesavulu, Kattela;
Kubaev, Aziz;
Taher, Waam Mohammed;
Alwan, Mariem;
Jawad, Mahmood Jasem;
Ali Al-Nuaimi, Ali M.;
Farhood, Bagher

Publication type:

Article

Virtual screening, optimization design, and synthesis analysis of novel benzofuran derivatives as pan-genotypic HCV NS5B polymerase inhibitors using molecular modeling.

Published in:

BMC Chemistry, 2025, v. 19, n. 1, p. 1, doi. 10.1186/s13065-025-01575-2

By:

Han, Di;
Xue, Yiwei;
Zhao, Fang;
Liu, Fengxiang;
Xia, Hongcheng;
Lu, Jiarui;
Wang, Meiting;
Liu, Taigang;
Cui, Shaoli;
Zhao, Junqiang;
Zhao, Zongya;
Gao, Qinghe;
Cui, Wei;
Xu, Yongtao

Publication type:

Article

In vitro investigation of the toxicological mechanisms of Fingolimod (S)-phosphate in HEPG2 cells Open Access.

Published in:

Toxicology Research, 2025, v. 14, n. 3, p. 1, doi. 10.1093/toxres/tfaf064

By:

Bilgehan, Ayşenur;
Şeker, Zehra;
Qaoud, Mohammed T;
Özhan, Gül

Publication type:

Article

Nucleic Acid Nanotechnology: Innovations Shaping the Future of Biomedicine and Diagnostics.

Published in:

Small Methods, 2025, v. 9, n. 6, p. 1, doi. 10.1002/smtd.202500756

By:

Yang, Dayong;
Mao, Chengde

Publication type:

Article

Imaging Ligand‐Receptor Interactions at Single‐Protein Resolution with DNA‐PAINT.

Published in:

Small Methods, 2025, v. 9, n. 6, p. 1, doi. 10.1002/smtd.202401799

By:

Honsa, Monique;
Pachmayr, Isabelle;
Heinze, Larissa;
Bas, Levent;
Masullo, Luciano A.;
Kwon, Jisoo;
Perovic, Ana;
Schulman, Brenda;
Jungmann, Ralf

Publication type:

Article

Systemic Brain Delivery of Oligonucleotide Therapeutics Enhanced by Protein Corona‐Assisted DNA Cubes.

Published in:

Small Methods, 2025, v. 9, n. 6, p. 1, doi. 10.1002/smtd.202400902

By:

Kim, Kyoung‐Ran;
Kang, Ji Hee;
Thai, Hien Bao Dieu;
Back, Ji Hyun;
Mao, Chengde;
Lee, Ji Eun;
Ko, Young Tag;
Ahn, Dae‐Ro

Publication type:

Article

3CL<sup>pro</sup> of SARS-CoV-2 as a new target for bufadienolides: in silico and in vitro study.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00623-2

By:

Kayumov, Muzaffar;
Razzokov, Jamoliddin;
Makhkamov, Mukhriddin;
Radjabov, Murodjon;
Mukhamedov, Nurkhodja;
Khakimov, Makhmudjon;
Asrorov, Akmal M.;
Khasanov, Okhunjon;
Yashinov, Ansor;
Tashmukhamedov, Mugrajitdin;
Wali, Ahmidin;
Yili, Abulimiti;
Mirzaakhmedov, Sharafitdin

Publication type:

Article

Quantum algorithm for protein-ligand docking sites identification in the interaction space.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00620-5

By:

Liliopoulos, Ioannis;
Varsamis, Georgios D.;
Karamanidou, Theodora;
Papalitsas, Christos;
Koulouras, Grigorios;
Pantazopoulos, Vassilios;
Stavropoulos, Thanos G.;
Karafyllidis, Ioannis G.

Publication type:

Article

Comment on "Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction" by Sun and Gao Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf163

By:

Krishnan, Sowmya Ramaswamy;
Roy, Arijit;
Gromiha, M Michael

Publication type:

Article

SYNTHESIS, CHARACTERIZATION, BSA BINDING ACTIVITY AND ADME PREDICTIONS OF A NEW Co(II) COMPLEX WITH O-VANILLIN-BASED SCHIFF BASE LIGAND.

Published in:

Mugla Journal of Science & Technology, 2025, v. 11, n. 1, p. 18, doi. 10.22531/muglajsci.1629497

By:

GÖKTÜRK, Tolga

Publication type:

Article

Discovery of Novel Potential Binders Targeting Norovirus 3CL Protease: A Machine Learning and Molecular Dynamics Approach.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 2, p. 257, doi. 10.1142/S2737416525500474

By:

Babaker, Manal A.;
Alatawi, Hanan Ali;
AlRashidi, Aljazi Abdullah;
Moglad, Ehssan;
Abdulhakim, Jawaher A.;
Afzal, Muhammad;
Babiker, M. A.;
Zeid, Isam M. Abu;
Altayb, Hisham N.

Publication type:

Article

Investigating the Anti-glioblastoma Potential of Alkaloids from the Solanaceae Family: A Multi-Targeted Approach Using Network Pharmacology and Molecular Modeling Approaches.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 2, p. 167, doi. 10.1142/S2737416525500425

By:

Alamri, Abdulaziz;
Jabir, Nasimudeen R.;
Firoz, Chelapram K.;
Alsolami, Khadeejah;
Khan, Mohd Shahnawaz;
Alhashmi, Mohammad Hassan;
Tabrez, Shams

Publication type:

Article

Systems Biology and Molecular Dynamics Approach for Identifying Synergistic Drug Combinations in Cancer Therapy.

Published in:

Journal of Computational Biophysics & Chemistry, 2026, v. 25, n. 1, p. 125, doi. 10.1142/S2737416525500401

By:

Ullah, Ihsan;
Firoz, Ahmad;
Anwar, Yasir;
Alghamdi, Khalid M. S.

Publication type:

Article

Computational Study of Coumarin Compounds as Potential Inhibitors of Casein Kinase 2: DFT, 2D-QSAR, ADMET and Molecular Docking Investigations.

Published in:

Polycyclic Aromatic Compounds, 2025, v. 45, n. 5, p. 843, doi. 10.1080/10406638.2024.2418408

By:

Chennai, Hind Yassmine;
Belaidi, Salah;
Ouassaf, Mebarka;
Sinha, Leena;
Prasad, Onkar;
Serdaroğlu, Goncagül;
Chtita, Samir

Publication type:

Article

Synthesis, Crystal Structure, Intermolecular Interactions, HOMO-LUMO, MEP, NLO Properties, and DFT/TD-DFT Investigation of (Z)-5-(4-Nitrobenzylidene)-3-N(3-Chlorophenyl)-2-Thioxothiazolidin-4-One.

Published in:

Polycyclic Aromatic Compounds, 2025, v. 45, n. 5, p. 810, doi. 10.1080/10406638.2024.2417717

By:

Belhachemi, Soumia;
Argoub, Kadda;
Rahmani, Rachida;
Boulakoud, Manel;
Djafri, Ahmed;
Kheddam, Narimane;
Tabti, Charef;
Toubal, Khaled;
Chouaih, Abdelkader

Publication type:

Article

Deep learning-based dipeptidyl peptidase IV inhibitor screening, experimental validation, and GaMD/LiGaMD analysis.

Published in:

BMC Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1186/s12915-025-02295-8

By:

He, Yi;
Zhang, Yan;
Liu, Minghao;
Li, Jiaying;
Li, Wannan;
Han, Weiwei

Publication type:

Article

An in silico evaluation of lorlatinib as a potential therapy for novel amino acid substitutions in the tyrosine kinase domain of the ALK protein associated with cancer.

Published in:

Frontiers in Pharmacology, 2025, p. 1, doi. 10.3389/fphar.2025.1605314

By:

Zapata Dongo, Richard Junior;
Poterico, Julio A.;
Fontana, Diletta;
Mologni, Luca;
Alvarez-Chacon, Carla;
Rojas-Armas, Juan;
Calla, Jaeson

Publication type:

Article

In-silico drug repositioning studies of Candida albicans Nitrogen permease reactivator 1 (Npr1) kinase.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08148-2

By:

Das, Sanjib;
Bagchi, Arka;
Bera, Analava;
Biswas, Arunima;
Roy, Analabha;
Ganguly, Rik;
Mondal, Amalesh;
Chattopadhyay, Deepanjan;
Mondal, Paromita Saha;
Mondal, Tanushree;
Samanta, Subhasree;
Goswami, Achintya Mohan;
Saha, Tanima

Publication type:

Article

Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-025-00613-4

By:

Porokhin, Vladimir;
Brown, Anne M.;
Hassoun, Soha

Publication type:

Article

Molecular Dynamics Study on Complexation of Uranyl and Zinc Ions with Fatty Acid Bound Human Serum Albumin.

Published in:

Liquids (2673-8015), 2025, v. 5, n. 2, p. 14, doi. 10.3390/liquids5020014

By:

Mishra, Vijayakriti;
Sawant, Pramilla D.;
Pathak, Arup Kumar

Publication type:

Article

Breathable Biomimetic Chiral Porous MOF Thin Films for Multiple Enantiomers Sensing.

Published in:

Advanced Functional Materials, 2025, v. 35, n. 26, p. 1, doi. 10.1002/adfm.202422860

By:

Li, Na;
Zhang, Jin‐Biao;
Wöll, Christof;
Gu, Zhi‐Gang;
Zhang, Jian

Publication type:

Article

In vitro and in silico investigations of Propolis-derived phytochemicals as potential inhibitors of Plasmodium falciparum.

Published in:

Veterinary World, 2025, v. 18, n. 6, p. 1644, doi. 10.14202/vetworld.2025.1644-1659

By:

Khan, Dhrubo Ahmed;
Nazmul Hasan, Md.;
Boonhok, Rachasak;
Sungkanu, Suthinee;
Singhaboot, Yutatirat;
Shorna, Afsana Amin;
Hasan, Anamul;
Chotivanich, Kesinee;
Wilairatana, Polrat;
Siyadatpanah, Abolghasem;
Norouzi, Roghayeh;
Sama-ae, Imran;
Mitsuwan, Watcharapong;
Paul, Alok K.;
de Lourdes Pereira, Maria;
Sundar, Shanmuga S.;
Mahboob, Tooba;
Wiart, Christophe;
Labana, Ryan V.;
Chimplee, Siriphorn

Publication type:

Article

Study of Retinoic Acid-Induced Osteoarthritis: Integrating RNA-Sequencing, Network Pharmacology, Molecular Docking, and Experimental Validation.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 12, p. 5519, doi. 10.3390/ijms26125519

By:

Lu, Tao;
Liu, Zi-Yi;
Ge, Yang-Shuo;
Jiang, Shuai-Yu;
Zhao, Qing-Ao;
Ding, Dao-Fang

Publication type:

Article

A computational study exploring echinoderm-derived compounds for inhibition of aminoglycoside acetyltransferases.

Published in:

PLoS ONE, 2025, v. 20, n. 7, p. 1, doi. 10.1371/journal.pone.0327409

By:

Alanzi, Abdullah R.;
Alqahtani, Moneerah J.;
Alqahtani, Jawaher H.;
Alharbi, Hattan A.

Publication type:

Article

A sialic acid-binding protein in Toxoplasma gondii contains a conserved globular domain in apicomplexan parasites.

Published in:

Parasites & Vectors, 2025, v. 18, n. 1, p. 1, doi. 10.1186/s13071-025-06845-5

By:

Sang, Xiaoyu;
Liu, Yize;
Zhang, Yiwei;
Chen, Ran;
Feng, Ying;
Jiang, Ning;
Chen, Qijun

Publication type:

Article

Editorial for Special Issue 'Engineering and Characterisation of Novel Nanomedicine Formulations, 2nd Edition'.

Published in:

2025

By:

Fernández-García, Raquel;
Bolás-Fernández, Francisco;
Fraguas-Sánchez, Ana Isabel

Publication type:

Editorial

Prognostic Modeling of Deleterious IDUA Mutations L238Q and P385R in Hurler Syndrome Through Molecular Dynamics Simulations.

Published in:

Pharmaceuticals (14248247), 2025, v. 18, n. 6, p. 922, doi. 10.3390/ph18060922

By:

Priya Nanda Kumar, Madhana;
Dharsini Selvamani, Esakki;
Pai Panemangalore, Archana;
Kumar Nanda Kumar, Sidharth;
Vasudevan, Vasundra;
Ramasamy, Magesh

Publication type:

Article

Exploring Brazilian Green Propolis Phytochemicals in the Search for Potential Inhibitors of B-Raf 600 E Enzyme: A Theoretical Approach.

Published in:

Pharmaceuticals (14248247), 2025, v. 18, n. 6, p. 902, doi. 10.3390/ph18060902

By:

de Souza, Garcia Ferreira;
Santana, Airis Farias;
Antunes, Fernanda Sanches Kuhl;
Cogo, Ramon Martins;
Pereira, Matheus Dornellas;
Rando, Daniela Gonçales Galasse;
Gonçalves, Carolina Passarelli

Publication type:

Article

DFT and Molecular Docking Study of HA-Conjugated SWCNTs for CD44-Targeted Delivery of Platinum-Based Chemotherapeutics.

Published in:

Pharmaceuticals (14248247), 2025, v. 18, n. 6, p. 805, doi. 10.3390/ph18060805

By:

Khan, Muhammad Uzair;
Jabeen, Ishrat;
Althagafi, Abdulhamid;
Farooq, Muhammad Umar;
Harb, Moussab;
Arkook, Bassim

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

Bacteriophages immobilized on electrospun cellulose microfibers by non-specific adsorption, protein-ligand binding, and electrostatic interactions.

Published in:

Cellulose, 2017, v. 24, n. 10, p. 4581, doi. 10.1007/s10570-017-1442-3

By:

Vonasek, Erica;
Lu, Ping;
Hsieh, You-Lo;
Nitin, Nitin

Publication type:

Article

Choice of ATP Analogues for Biophysical Studies—A Systematic NMR-Based Investigation for the AAA Enzyme p97.

Published in:

Biophysica, 2025, v. 5, n. 1, p. 9, doi. 10.3390/biophysica5010009

By:

Droemer, Maxim A.;
Shein, Mikhail;
Schütz, Anne K.

Publication type:

Article

Modeling the Interaction Between Silver(I) Ion and Proteins with 12-6 Lennard-Jones Potential: A Bottom-Up Parameterization Approach †.

Published in:

Biophysica, 2025, v. 5, n. 1, p. 7, doi. 10.3390/biophysica5010007

By:

Manciocchi, Luca;
Bianchi, Alexandre;
Mazan, Valérie;
Potapov, Mark;
Fromm, Katharina M.;
Spichty, Martin

Publication type:

Article

Gibbs Free Energy and Enthalpy–Entropy Compensation in Protein Folding.

Published in:

Biophysica, 2025, v. 5, n. 1, p. 2, doi. 10.3390/biophysica5010002

By:

Benítez, María J.;
Jiménez, Juan S.

Publication type:

Article

Gibbs Free Energy and Enthalpy–Entropy Compensation in Protein–Ligand Interactions.

Published in:

Biophysica, 2024, v. 4, n. 2, p. 298, doi. 10.3390/biophysica4020021

By:

Jiménez, Juan S.;
Benítez, María J.

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

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

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

Gen-AI Methods, Molecular Docking and Molecular Dynamics Simulations for Identification of Novel Inhibitors of MmPL3 Transporter of Mycobacterium tuberculosis.

Published in:

Journal of Computational Biophysics & Chemistry, 2025, v. 24, n. 4, p. 471, doi. 10.1142/S2737416524500674

By:

Pawar, Atul;
Almutairi, Tahani Mazyad;
Shinde, Omkar;
Chikhale, Rupesh

Publication type:

Article

Network Analysis and In Silico Molecular Modeling of Bioactive Compounds from Sida cordifolia Against NMDA Receptor.

Published in:

Journal of Computational Biophysics & Chemistry, 2025, v. 24, n. 3, p. 307, doi. 10.1142/S273741652341003X

By:

Murali, Cibe Chakaravarthy;
Kunjiappan, Selvaraj;
Murugesan, Sankaranarayanan;
Pandian, Sureshbabu Ram Kumar;
Kathiresan, Thandavarayan;
Sundar, Krishnan

Publication type:

Article

In Silico Studies of (Z)-3-(2-Chloro-4-Nitrophenyl)-5-(4-Nitrobenzylidene)-2-Thioxothiazolidin-4-One Derivatives as PPAR-γ Agonist: Design, Molecular Docking, MM-GBSA Assay, Toxicity Predictions, DFT Calculations and MD Simulation Studies.

Published in:

Journal of Computational Biophysics & Chemistry, 2024, v. 23, n. 1, p. 117, doi. 10.1142/S2737416523500540

By:

Srinivasa, Mahendra Gowdru;
Shivakumar;
Kumar, D. Udaya;
Mehta, Chetan Hasmukh;
Nayak, Usha Yogendra;
Revanasiddappa, B. C.

Publication type:

Article

A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies.

Published in:

Journal of Computational Biophysics & Chemistry, 2022, v. 21, n. 3, p. 259, doi. 10.1142/S2737416522300012

By:

Ridhwan, Mohamad Jemain Mohamad;
Bakar, Syahrul Imran Abu;
Latip, Normala Abd;
Ghani, Nurunajah Ab;
Ismail, Nor Hadiani

Publication type:

Article

Virtual drug screening study to discover novel ERAP1 allosteric site inhibitors for the treatment of ankylosing spondylitis (AS).

Published in:

Journal of Research in Pharmacy, 2025, v. 29, n. 2, p. 530, doi. 10.12991/jrespharm.1661031

By:

PORTAKAL, Hüseyin Saygın;
ALP, Beste;
AKYOL, Mertcan

Publication type:

Article

IN VITRO AND IN SILICO EVALUATION OF THE ANTIVIRAL POTENTIAL OF EUCALYPTUS ESSENTIAL OILS.

Published in:

Journal of Research in Pharmacy, 2023, v. 27, p. 21, doi. 10.29228/jrp.578

By:

AK-SAKALLI, Ezgi;
KARADAĞ, Ayşe Esra;
TERALI, Kerem;
ÇELİK, İsmail;
KOŞAR, Müberra;
DEMİRCİ, Fatih

Publication type:

Article

Pharmacophore-based Virtual Screening: Identification of Selective Sirtuin 2 Inhibitors.

Published in:

Journal of Research in Pharmacy, 2023, v. 27, n. 4, p. 1366, doi. 10.29228/jrp.424

By:

KARAMAN MAYACK, Berin;
ALAYOUBI, Muhammed Moyasar

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

Clustered peptide regulating the multivalent interaction between RANK and TRAF6 inhibits osteoclastogenesis by fine-tuning signals.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-08047-2

By:

Anzai, Masataka;
Watanabe-Takahashi, Miho;
Kawabata, Hiroshi;
Masuda, Yuri;
Ikegami, Aoi;
Okuda, Yuta;
Waku, Tsuyoshi;
Sakurai, Hiroaki;
Nishikawa, Keizo;
Inoue, Jun-ichiro;
Nishikawa, Kiyotaka

Publication type:

Article