Results 101 to 110 of about 11,503 (243)

Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47–55

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT The HADDOCK team participated in CAPRI rounds 47–55 as server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 ...
Victor Reys, Marco Giulini, Vlad Cojocaru, Anna Engel, Xiaotong Xu, Jorge Roel‐Touris, Cunliang Geng, Francesco Ambrosetti, Brian Jiménez‐García, Zuzana Jandova, Panagiotis I. Koukos, Charlotte van Noort, João M. C. Teixeira, Siri C. van Keulen, Manon Réau, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin   +16 more
wiley   +1 more source

Targeting mGlyR with nanobodies for depression

Nature Communications
Abstract Development of therapies for neuropsychiatric conditions is one of the greatest challenges of modern medicine. Common limitations of traditional small molecule drugs include poor efficacy, off-target side effects and difficult druggability of many targets.
Laboute, Thibaut, Zucca, Stefano, Sial, Omar, Sharma, Mansi, Brunori, Gloria, Singh, Shikha, Nageswar, Kv, Peng, Haiyong, Rader, Christoph, Becker, Jérôme Aj, Le Merrer, Julie, Singh, Appu, Martemyanov, Kirill   +12 more
openaire   +3 more sources

AlphaFold and Docking Approaches for Antibody–Antigen and Other Targets: Insights From CAPRI Rounds 47–55

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT Accurate modeling of the structures of protein–protein complexes and other biomolecular interactions represents a longstanding and important challenge for computational biology. The Critical Assessment of PRedicted Interactions (CAPRI) experiment has served for over two decades as a key means to assess and compare current approaches and ...
Ragul Gowthaman, Minjae Park, Rui Yin, Johnathan D. Guest, Brian G. Pierce   +4 more
wiley   +1 more source

Massive Sampling Strategy for Antibody–Antigen Targets in CAPRI Round 55 With MassiveFold

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT Massive sampling with AlphaFold2 improves protein–protein complex predictions. This has been shown during the last CASP15‐CAPRI blind prediction round by the AFsample tool. However, more difficult targets including antibody–antigen binding remain challenging. CAPRI Round 55 consisted of three antibody–antigen targets and one heterotrimer.
Nessim Raouraoua, Marc F. Lensink, Guillaume Brysbaert   +2 more
wiley   +1 more source

Ultrapotent Broadly Neutralizing Human‐llama Bispecific Antibodies against HIV‐1

Advanced Science
Broadly neutralizing antibodies are proposed as therapeutic and prophylactic agents against HIV‐1, but their potency and breadth are less than optimal.
Jianliang Xu, Tongqing Zhou, Krisha McKee, Baoshan Zhang, Cuiping Liu, Alexandra F. Nazzari, Amarendra Pegu, Chen‐Hsiang Shen, Jordan E. Becker, Michael F. Bender, Payton Chan, Anita Changela, Ridhi Chaudhary, Xuejun Chen, Tal Einav, Young Do Kwon, Bob C. Lin, Mark K. Louder, Jonah S. Merriam, Nicholas C. Morano, Sijy O'Dell, Adam S. Olia, Reda Rawi, Ryan S. Roark, Tyler Stephens, I‐Ting Teng, Emily Tourtellott‐Fogt, Shuishu Wang, Eun Sung Yang, Lawrence Shapiro, Yaroslav Tsybovsky, Nicole A. Doria‐Rose, Rafael Casellas, Peter D. Kwong   +33 more
doaj   +1 more source

Improving the production and stability of nanobodies

Protein Engineering, Design and Selection
Abstract Nanobodies offer unique advantages in biomedical and biotechnological applications due to their smaller size, ability to bind challenging epitopes, and affordable production using recombinant technology. However, challenges in large-scale production, stability, and solubility limit their widespread use.
Alba Pejenaute, Laura Gálvez-Larrosa, Cristina M Segovia, Pablo Herrero-Alfonso, David Fernández-Ramos, Fernando Lopitz-Otsoa, Óscar Millet, Francesca Peccati, Gonzalo Jiménez-Osés, Gabriel Ortega-Quintanilla   +9 more
openaire   +2 more sources

Biomolecular Interaction Prediction in the Pre‐ and Post‐AlphaFold Era: The 8th CAPRI Evaluation

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID‐related Rounds), which have witnessed the transition to AI‐driven prediction tools such as AlphaFold and related alternatives. The prediction Rounds in this evaluation are characterized by a high level of difficulty due
Marc F. Lensink, Nessim Raouraoua, Guillaume Brysbaert, Sameer Velankar, Shoshana J. Wodak, Alexandre M. J. J. Bonvin   +5 more
wiley   +1 more source

Performance of pyDock in 8th CAPRI: Energy‐Based Scoring Applied to Docking and AlphaFold Models

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT The 8th CAPRI edition has shown a significant evolution in the field of protein–protein complex structure prediction. We have participated in all 11 targets proposed in this edition, involving domain‐domain, protein–protein, protein‐peptide, and protein‐DNA interactions, including homo‐ and hetero‐meric interfaces.
Luis Angel Rodríguez‐Lumbreras, Mireia Rosell, Miguel Romero‐Durana, Víctor Monteagudo, Fabian Glaser, Juan Fernandez‐Recio   +5 more
wiley   +1 more source

Targeting the CD47–SIRPα phagocytic checkpoint in cancer: Biology, translational opportunities, and next‐generation therapeutic strategies

Smart Molecules, EarlyView.
The CD47–SIRPα axis has emerged as a critical innate immune checkpoint that suppresses macrophage‐mediated phagocytosis through a canonical “don't eat me” signal and enables tumor immune evasion. We comprehensively summarize the structural and biological features of CD47 and the molecular mechanisms underlying CD47‐mediated regulation of phagocytosis ...
Ruimei Zhou, Lingjie Jing, Jianping Zhang, Cheng Guo, Quanjun Yang   +4 more
wiley   +1 more source

Recent Advances in Photocatalyst‐Driven Protein Labeling and Proximity Mapping

The Chemical Record, EarlyView.
Photocatalyst‐driven protein labeling and proximity mapping have rapidly advanced as powerful strategies for spatiotemporal control in complex biological environments. This review integrates recent developments across single‐electron transfer and energy transfer‐based mechanisms and highlights how catalyst design, reactive intermediates, and diffusion ...
Shinichi Sato, Kazuki Miura, Juki Nakao, Hiroyuki Nakamura   +3 more
wiley   +1 more source