Works matching Ligands (Biochemistry)

Results: 5000

Reversible Ligand Binding Reactions: WHY DO BIOCHEMISTRY STUDENTS HAVE TROUBLE CONNECTING THE DOTS?

Published in:

Biochemistry & Molecular Biology Education, 2007, v. 35, n. 2, p. 105, doi. 10.1002/bmb.29

By:

Sears, Duane W.;
Thompson, Scott E.;
Saxon, S. Robin

Publication type:

Article

Impact of Conformational Substates and Energy Landscapes on Understanding Hemoglobin Kinetics and Function.

Published in:

Journal of Biological Physics, 2021, v. 47, n. 4, p. 337, doi. 10.1007/s10867-021-09588-3

By:

Eaton, William A.

Publication type:

Article

Proteome‐Wide Ligand and Target Discovery by Using β‐Nitrostyrene Electrophiles: Supporting Targeted Protein Degradation.

Published in:

Angewandte Chemie, 2025, v. 137, n. 32, p. 1, doi. 10.1002/ange.202504813

By:

Ouyang, Xinyao;
Chai, Xiaomeng;
Huang, Lei;
Chen, Yubin;
Li, Shengrong;
Huang, Weizhen;
Li, Yifang;
Ding, Ke;
Liu, Tongzheng;
Tan, Yi;
Li, Zhengqiu

Publication type:

Article

Capturing Peptide–GPCR Interactions and Their Dynamics.

Published in:

Molecules, 2020, v. 25, n. 20, p. 4724, doi. 10.3390/molecules25204724

By:

Kaiser, Anette;
Coin, Irene;
Ruzza, Paolo

Publication type:

Article

Application of 4D-QSAR Studies to a Series of Raloxifene Analogs and Design of Potential Selective Estrogen Receptor Modulators.

Published in:

Molecules, 2012, v. 17, n. 6, p. 7415, doi. 10.3390/molecules17067415

By:

Sodero, Ana Carolina Rennó;
Romeiro, Nelilma Correia;
Da Cunha, Elaine Fontes Ferreira;
De Oliveira Magalhães, Uiaran;
De Alencastro, Ricardo Bicca;
Rodrigues, Carlos Rangel;
Cabral, Lúcio Mendes;
Castro, Helena Carla;
Albuquerque, Magaly Girão

Publication type:

Article

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

Published in:

Bioinformatics, 2015, v. 31, n. 4, p. 539, doi. 10.1093/bioinformatics/btu692

By:

Roy, Ambrish;
Skolnick, Jeffrey

Publication type:

Article

The cAMP receptor protein from Gardnerella vaginalis is not regulated by ligands.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06957-1

By:

Dong, Hongjie;
Zhang, Junmei;
Zhang, Kundi;
Zhang, Fengyu;
Wang, Shuai;
Wang, Qi;
Xu, Chao;
Yin, Kun;
Gu, Lichuan

Publication type:

Article

Ligand-induced shifts in conformational ensembles that describe transcriptional activation.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.80140

By:

Khan, Sabab Hasan;
Braet, Sean M.;
Koehler, Stephen John;
Elacqua, Elizabeth;
Anand, Ganesh Srinivasan;
Okafor, C. Denise

Publication type:

Article

Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields.

Published in:

Life (2075-1729), 2022, v. 12, n. 1, p. 54, doi. 10.3390/life12010054

By:

Byun, Jinyoung;
Lee, Juyong

Publication type:

Article

A non-canonical mechanism of GPCR activation.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-54103-6

By:

Powers, Alexander S.;
Khan, Aasma;
Paggi, Joseph M.;
Latorraca, Naomi R.;
Souza, Sarah;
Di Salvo, Jerry;
Lu, Jun;
Soisson, Stephen M.;
Johnston, Jennifer M.;
Weinglass, Adam B.;
Dror, Ron O.

Publication type:

Article

Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2.

Published in:

Bioinformatics & Biology Insights, 2021, p. 1, doi. 10.1177/11779322211018200

By:

Aktas, Emre

Publication type:

Article

Ligand-Receptor Interactions and Drug Design.

Published in:

Biochemistry Insights, 2015, v. 8, p. 1, doi. 10.4137/BCI.S37978

By:

Zhang, Yanling;
Song, Jianrui;
Zhang, Xiaojun;
Xiao, Yuanyuan

Publication type:

Article

Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy.

Published in:: Biotechnology for Biofuels, 2012, v. 5, n. 1, p. 3, doi. 10.1186/1754-6834-5-3
Publication type:: Article

Molecular Mechanism of the Drop in the pKa of a Substrate Analog Bound to Medium-Chain Acyl-CoA Dehydrogenase: Implications for Substrate Activation.

Published in:

Journal of Biochemistry, 2003, v. 134, n. 6, p. 835, doi. 10.1093/jb/mvg209

By:

Nishina, Yasuzo;
Sato, Kyosuke;
Tamaoki, Haruhiko;
Tanaka, Takeyuki;
Setoyama, Chiaki;
Miura, Retsu;
Shiga, Kiyoshi

Publication type:

Article

Demonstration of the pH Sensitive Binding of Multivalent Carbohydrate Ligands to Immobilized Shiga-Like Toxin 1 B Subunits1.

Published in:

Journal of Biochemistry, 2001, v. 130, n. 5, p. 665, doi. 10.1093/oxfordjournals.jbchem.a003032

By:

Imai, Yasuyuki;
Matsuura, Yasumi;
Ono, Yousuke;
Ishikawa, Tomoyuki;
Ito, Yukishige

Publication type:

Article

Binding‐Site Purification of Actives (B‐SPA) Enables Efficient Large‐Scale Progression of Fragment Hits by Combining Multi‐Step Array Synthesis With HT Crystallography.

Published in:

Angewandte Chemie, 2025, v. 137, n. 16, p. 1, doi. 10.1002/ange.202424373

By:

Grosjean, Harold;
Aimon, Anthony;
Hassell‐Hart, Storm;
Thompson, Warren;
Koekemoer, Lizbé;
Bennett, James;
Bradley, Anthony;
Anderson, Cameron;
Wild, Conor;
Bradshaw, William J.;
FitzGerald, Edward A.;
Krojer, Tobias;
Fedorov, Oleg;
Biggin, Philip C.;
Spencer, John;
von Delft, Frank

Publication type:

Article

A Hierarchical Approach to Cooperativity in Macromolecular and Self-Assembling Binding Systems.

Published in:

Journal of Biological Physics, 2008, v. 34, n. 1/2, p. 213, doi. 10.1007/s10867-008-9116-x

By:

Garcés, Josep;
Acerenza, Luis;
Mizraji, Eduardo;
Mas, Francesc

Publication type:

Article

Poster Presentations.

Published in:: Journal of Labelled Compounds & Radiopharmaceuticals, 2017, v. 60, p. 111, doi. 10.1002/jlcr.3508
Publication type:: Article

Molecular Recognition and Modification Strategies of Umami Dipeptides with T1R1/T1R3 Receptors.

Published in:

Molecules, 2025, v. 30, n. 13, p. 2774, doi. 10.3390/molecules30132774

By:

Hu, Kaixuan;
Sun, Guangzhou;
Yu, Wentong;
Zhang, Mengyu;
Wang, Shuang;
Cao, Yujie;
Hu, Dongling;
Liang, Li;
He, Gang;
Hu, Jianping;
Liu, Wei

Publication type:

Article

Design and Synthesis of D 3 R Bitopic Ligands with Flexible Secondary Binding Fragments: Radioligand Binding and Computational Chemistry Studies.

Published in:

Molecules, 2024, v. 29, n. 1, p. 123, doi. 10.3390/molecules29010123

By:

Tian, Gui-Long;
Hsieh, Chia-Ju;
Taylor, Michelle;
Lee, Ji Youn;
Luedtke, Robert R.;
Mach, Robert H.

Publication type:

Article

Systematic Modification of the Substitution Pattern of the 7-Hydroxy-5-oxopyrazolo[4,3- b ]pyridine-6-carboxamide Scaffold Enabled the Discovery of New Ligands with High Affinity and Selectivity for the Cannabinoid Type 2 Receptor.

Published in:

Molecules, 2023, v. 28, n. 13, p. 4958, doi. 10.3390/molecules28134958

By:

Mugnaini, Claudia;
Kostrzewa, Magdalena;
Casini, Marta;
Kumar, Poulami;
Catallo, Valeria;
Allarà, Marco;
Guastaferro, Laura;
Brizzi, Antonella;
Paolino, Marco;
Tafi, Andrea;
Kapatais, Christelos;
Giorgi, Gianluca;
Vacondio, Federica;
Mor, Marco;
Corelli, Federico;
Ligresti, Alessia

Publication type:

Article

Novel Xanomeline-Containing Bitopic Ligands of Muscarinic Acetylcholine Receptors: Design, Synthesis and FRET Investigation.

Published in:

Molecules, 2023, v. 28, n. 5, p. 2407, doi. 10.3390/molecules28052407

By:

Matera, Carlo;
Kauk, Michael;
Cirillo, Davide;
Maspero, Marco;
Papotto, Claudio;
Volpato, Daniela;
Holzgrabe, Ulrike;
De Amici, Marco;
Hoffmann, Carsten;
Dallanoce, Clelia

Publication type:

Article

Cyclic-di-GMP and ADP bind to separate domains of PilB as mutual allosteric effectors.

Published in:

Biochemical Journal, 2020, v. 477, n. 1, p. 213, doi. 10.1042/BCJ20190809

By:

Dye, Keane J.;
Zhaomin Yang

Publication type:

Article

In Silico Study of Potential Small Molecule TIPE2 Inhibitors for the Treatment of Cancer.

Published in:

Sci (2413-4155), 2023, v. 5, n. 4, p. 39, doi. 10.3390/sci5040039

By:

Wilson, Jerica;
Evangelou, Katerina;
Chen, Youhai H.;
Ji, Hai-Feng

Publication type:

Article

Cloning and molecular modeling of free fatty acid receptor GPCR 43 with dietary flavonoids as novel ligands.

Published in:

Kuwait Journal of Science, 2023, v. 50, n. 1A, p. 1

By:

Ihtsham, Arooma;
Hayat, Rida;
Khan, Fariha

Publication type:

Article

Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with β-substituted disaccharides.

Published in:

IUBMB Life, 2017, v. 69, n. 2, p. 72, doi. 10.1002/iub.1593

By:

Abhinav, K. V.;
Sharma, Kaushal;
Surolia, A.;
Vijayan, Mamannamana

Publication type:

Article

Comparative evaluation of methods for the prediction of protein–ligand binding sites.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00923-z

By:

Utgés, Javier S.;
Barton, Geoffrey J.

Publication type:

Article

Does the urokinase receptor exist in a latent form?

Published in:

Cellular & Molecular Life Sciences, 2007, v. 64, n. 9, p. 1033, doi. 10.1007/s00018-007-6498-z

By:

Yuan, C.;
Huang, M.

Publication type:

Article

Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations.

Published in:

Cellular & Molecular Life Sciences, 2004, v. 61, n. 7/8, p. 783, doi. 10.1007/s00018-003-3406-z

By:

Klebe, G.;
Krämer, O.;
Sotriffer, C.

Publication type:

Article

The CD40/CD154 receptor/ligand dyadRID="†"ID="†" Review.

Published in:

Cellular & Molecular Life Sciences, 2001, v. 58, n. 1, p. 4

By:

Schönbeck, U.;
Libby, P.

Publication type:

Article

The role of glycosylation in ionotropic glutamate receptor ligand binding, function, and trafficking.

Published in:

Cellular & Molecular Life Sciences, 2000, v. 57, n. 11, p. 1508, doi. 10.1007/PL00000635

By:

Standley, S.;
Baudry, M.

Publication type:

Article

Enhancement of enzyme efficiency and stability by incorporation of unnatural amino acid residues in a targeted functional site.

Published in:

FASEB Journal, 2007, v. 21, n. 6, p. A1012

By:

Hegazy, Usama M.;
Mannervik, Bengt

Publication type:

Article

A danger of low copy numbers for inferring incorrect cooperativity degree.

Published in:

Theoretical Biology & Medical Modelling, 2010, v. 7, p. 40, doi. 10.1186/1742-4682-7-40

By:

Konkoli, Zoran

Publication type:

Article

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Published in:

BMC Bioinformatics, 2012, v. 13, n. Suppl 4, p. 1, doi. 10.1186/1471-2105-13-S4-S17

By:

Bianchi, Valerio;
Gherardini, Pier Federico;
Helmer-Citterich, Manuela;
Ausiello, Gabriele

Publication type:

Article

Constructing patch-based ligand-binding pocket database for predicting function of proteins.

Published in:

BMC Bioinformatics, 2012, v. 13, n. Suppl 2, p. 1, doi. 10.1186/1471-2105-13-S2-S7

By:

Sael, Lee;
Kihara, Daisuke

Publication type:

Article

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.

Published in:

BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S35

By:

Totrov, Maxim

Publication type:

Article

Virtual screening of GPCRs: An in silico chemogenomics approach.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-363

By:

Jacob, Laurent;
Hoffmann, Brice;
Stoven, Véronique;
Vert, Jean-Philippe

Publication type:

Article

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005787

By:

Gygli, Gudrun;
Lucas, Maria Fátima;
Guallar, Victor;
van Berkel, Willem J. H.

Publication type:

Article

Regulated Proteolysis of NOTCH2 and NOTCH3 Receptors by ADAM10 and Presenilins.

Published in:

Molecular & Cellular Biology, 2014, v. 34, n. 15, p. 2822, doi. 10.1128/MCB.00206-14

By:

Groot, Arjan J.;
Habets, Roger;
Yahyanejad, Sanaz;
Hodin, Caroline M.;
Reiss, Karina;
Saftig, Paul;
Theys, Jan;
Vooijs, Marc

Publication type:

Article

Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets.

Published in:

Journal of Computer-Aided Molecular Design, 2007, v. 21, n. 9, p. 539, doi. 10.1007/s10822-007-9137-8

By:

Polgár, Tímea;
Menyhárd, Dóra;
Keserű, György

Publication type:

Article

ENPDA: an evolutionary structure-based de novo peptide design algorithm.

Published in:

Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 8, p. 585, doi. 10.1007/s10822-005-9015-1

By:

Belda, Ignasi;
Madurga, Sergio;
Llorà, Xavier;
Martinell, Marc;
Tarragó, Teresa;
Piqueras, Mireia;
Nicolás, Ernesto;
Giralt, Ernest

Publication type:

Article

In-silico Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach.

Published in:

Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 4, p. 213, doi. 10.1007/s10822-005-4788-9

By:

Sivanesan, Dakshanamurthy;
Rajnarayanan, Rajendram V.;
Doherty, Jason;
Pattabiraman, Nagarajan

Publication type:

Article

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase.

Published in:

Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 3, p. 165, doi. 10.1007/s10822-005-3693-6

By:

Alonso, Hernán;
Gillies, Malcolm;
Cummins, Peter;
Bliznyuk, Andrey;
Gready, Jill

Publication type:

Article

The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.

Published in:

Journal of Computer-Aided Molecular Design, 2004, v. 18, n. 2, p. 89, doi. 10.1023/B:jcam.0000030032.81753.b4

By:

Lloyd, David G.;
Garcia-Sosa, Alfonso T.;
Alberts, Ian L.;
Todorov, Nikolay P.;
Mancera, Ricardo L.

Publication type:

Article

Comparative study of several algorithms for flexible ligand docking.

Published in:

Journal of Computer-Aided Molecular Design, 2003, v. 17, n. 11, p. 755, doi. 10.1023/B:JCAM.0000017496.76572.6f

By:

Bursulaya, Badry D.;
Totrov, Maxim;
Abagyan, Ruben;
Brooks III, Charles L.

Publication type:

Article

Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules.

Published in:

Bioinformatics, 2010, v. 26, n. 8, p. 1022, doi. 10.1093/bioinformatics/btq084

By:

Wei-Yao Chou;
Wei-I Chou;
Tun-Wen Pai;
Shu-Chuan Lin;
Ting-Ying Jiang;
Chuan-Yi Tang;
Dah-Tsyr Chang, Margaret

Publication type:

Article

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding.

Published in:

Bioinformatics, 2009, v. 25, n. 5, p. 615, doi. 10.1093/bioinformatics/btp035

By:

Izhar Wallach;
Ryan Lilien

Publication type:

Article

TRITON: a graphical tool for ligand-binding protein engineering.

Published in:

Bioinformatics, 2008, v. 24, n. 17, p. 1955, doi. 10.1093/bioinformatics/btn344

By:

Prokop, Martin;
Adam, Jan;
Kříž, Zdeněek;
Wimmerová, Michaela;
Kočca, Jaroslav

Publication type:

Article

Allosteric response to ligand binding: Molecular dynamics study of the N-terminal domains in IP<sub>3</sub> receptor.

Published in:

Biophysics & Physicobiology, 2019, v. 16, n. 1, p. 232, doi. 10.2142/biophysico.16.0_232

By:

Kei Moritsugu;
Tsubasa Ito;
Akinori Kidera

Publication type:

Article

Methyl probes in proteins for determining ligand binding mode in weak protein–ligand complexes.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-13561-y

By:

Mohanty, Biswaranjan;
Orts, Julien;
Wang, Geqing;
Nebl, Stefan;
Alwan, Wesam S.;
Doak, Bradley C.;
Williams, Martin L.;
Heras, Begoña;
Mobli, Mehdi;
Scanlon, Martin J.

Publication type:

Article