相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。
Article
Computer Science, Artificial Intelligence
Kai Han et al.
Summary: Transformer, a deep neural network with a self-attention mechanism, has been initially used in natural language processing and is now gaining attention in computer vision tasks. Transformer-based models perform as well as or even better than convolutional and recurrent neural networks in various visual benchmarks. This paper reviews vision transformer models, categorizes them based on different tasks, and analyzes their advantages and disadvantages. The discussed categories include backbone network, high/mid-level vision, low-level vision, and video processing. Efficient methods for applying transformer in real device-based applications are also explored. The challenges and further research directions for vision transformers are discussed as well.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Chemistry, Medicinal
Yong Xiao Yang et al.
Summary: Protein-protein binding affinity is crucial for understanding protein functions and designing protein-based therapeutics. A web server called AREA-AFFINITY has been developed for predicting protein-protein or antibody-protein antigen binding affinity based on the geometric characteristics of interface and surface areas in protein-protein complexes. The server implements multiple predictive models and performs better compared to existing methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Jeffrey A. Ruffolo et al.
Summary: Antibodies have the ability to bind diverse antigens, making them critical for therapeutics and diagnostics. IgFold is a fast deep learning method that accurately predicts antibody structures, providing insights for a larger number of antibodies compared to experimental methods.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Victor L. Cruz et al.
Summary: The binding affinity of trastuzumab and pertuzumab to HER2 was studied using experimental and computational methods. The experiments were conducted using complete IgG antibodies and the extracellular domain of HER2 in solution. The results showed that pertuzumab had slightly higher binding affinity than trastuzumab, possibly due to different interfacial contact descriptors. Furthermore, the experiments revealed that pertuzumab preferred to bind to two HER2 proteins, while trastuzumab mainly formed a monovalent complex, possibly due to steric crowding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Minhyeok Lee
Article
Biochemical Research Methods
Yoochan Myung et al.
Summary: The study developed a machine learning method CSM-AB capable of predicting antibody-antigen binding affinity and accurately ranking near-native poses, showing promising results for the development of new immunotherapies.
Article
Biochemical Research Methods
Brennan Abanades et al.
Summary: In this study, the researchers developed a deep learning-based tool called ABlooper for predicting the structure of CDR loops in antibodies. ABlooper accurately predicts the structure of CDR-H3 loops, which are known for their sequence and structural variability. The tool provides high accuracy predictions and confidence estimates for each prediction.
Article
Biochemistry & Molecular Biology
Constantin Schneider et al.
Summary: The Structural Antibody Database (SAbDab) was released in 2013 as a publicly available repository of experimentally determined antibody structures. In response to the growing interest in antibodies as biotherapeutics, the database has implemented improvements such as the development of SAbDab-nano, a sub-database tracking nanobodies. Both databases are updated weekly, annotated with the latest features, and freely accessible online.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Tobias H. Olsen et al.
Summary: The antibody repertoires are crucial for exploring disease states, vaccine responses, and therapeutic development, but accessing and processing data remains a challenge. The OAS database provides clean, annotated, and translated antibody repertoire data, with updates to accommodate increasing data volume and paired sequencing data. OAS now offers a new web server and standardized search parameters, making it a valuable resource.
Article
Mohammed Ali Bakkari et al.
Recent Patents on Biotechnology
(2022)
Review
Pharmacology & Pharmacy
Yiming Jin et al.
Summary: Antibody-drug conjugates (ADCs) are cancer therapeutic agents that utilize the specificity of antibodies to target toxic drugs to tumor cells. The recent clinical development of ADCs has shown an increasing trend, with more approved drugs in the market. The in vivo processing of ADCs plays a crucial role in their design and efficacy.
PHARMACOLOGY & THERAPEUTICS
(2022)
Review
Parasitology
Lars Hviid et al.
Summary: IgG antibodies play a key role in acquired immunity to Plasmodium falciparum malaria and their antigen specificity has been a major research focus. However, recent findings show that naturally induced PfEMP1-specific IgG1 has a selectively modified Fc domain, resulting in afucosylated IgG with increased affinity for Fc gamma RIII found on natural killer cells. These findings have implications for understanding antimalarial immunity and designing improved vaccines.
TRENDS IN PARASITOLOGY
(2022)
Review
Infectious Diseases
Daniele Focosi et al.
Summary: This paper reviews the use of monoclonal antibodies (mAbs) targeting the spike protein of SARS-CoV-2 in the ongoing COVID-19 pandemic and discusses their therapeutic effects, structural classification, immune escape, and limitations. It also explores the impact of the Omicron variant on treatment strategies and potential future developments for improved outcomes.
LANCET INFECTIOUS DISEASES
(2022)
Review
Biotechnology & Applied Microbiology
Simone C. Oostindie et al.
Summary: This review discusses the role of avidity in eliciting antibody functional responses and current engineering strategies for manipulating avidity interactions in antibody-based therapies. Avidity, derived from multiple affinity interactions, is fundamental to all aspects of antibody biology and is crucial for enhancing or engineering novel properties in antibody biotherapeutics. Therapeutic antibody mechanisms of action are comprehensively reviewed with an emphasis on engineered optimizations and platforms, leading to a new wave of differentiated antibody drugs with tailored properties and promising improved treatment options for various diseases.
NATURE REVIEWS DRUG DISCOVERY
(2022)
Article
Mathematical & Computational Biology
Zhongliang Guo et al.
Summary: Protein-protein interactions play a crucial role in biological activity. The rapid development of machine learning methods for predicting protein-protein binding affinity has opened up new possibilities for protein design.
FRONTIERS IN BIOINFORMATICS
(2022)
Review
Cell Biology
Yu-Chyi Hwang et al.
Summary: The COVID-19 pandemic has created a public health crisis, leading to the urgent development of therapeutic treatments and virus detection methods. Monoclonal antibodies (mAbs) have emerged as powerful tools for treating and detecting diseases due to their high specificity and reliability. Researchers are urgently developing antibody-based kits for SARS-CoV-2 detection and antibody drugs for COVID-19 treatment. The spike protein of SARS-CoV-2, which is crucial for viral infection, has been extensively studied and its receptor-binding domain (RBD) has become a major target for therapeutic antibody development. Given the high mutation rate of SARS-CoV-2, especially under the pressure of prophylactic vaccines and neutralizing antibodies, the use of antibody cocktails is expected to be an important strategy for effective COVID-19 treatment. Additionally, antibodies against cytokine storms, which can be triggered by SARS-CoV-2 infection and drive severe disease progression, are also being developed as treatments for COVID-19. In addition to their use as drugs, antibodies are currently being used in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests, which are crucial surveillance tools for preventing the spread of COVID-19.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Syed Mohammed Basheeruddin Asdaq et al.
Summary: The focus of the study is on developing monoclonal antibodies as a treatment option for SARS-CoV-2, targeting the interaction between the virus and host cells. Some monoclonal antibodies have already received emergency use authorization and are being used for high-risk patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Carlos Cruz-Teran et al.
Summary: The article discusses the global efforts to combat the COVID-19 pandemic with potent neutralizing mAbs and highlights the challenges faced by current antiviral mAbs. It also presents evidence supporting inhaled delivery of antiviral mAbs as an early intervention against COVID-19.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Review
Biochemistry & Molecular Biology
Jiayu Liao et al.
Summary: Protein-protein interactions are vital in life, and FRET is widely used to detect molecular interactions with high sensitivity and efficiency. Attempts to develop FRET into a quantitative measurement for interaction affinity have faced challenges, but the method shows great potential for studying difficult-to-express proteins and interactions in living cells.
Article
Biochemistry & Molecular Biology
Johnathan D. Guest et al.
Summary: The study aims to accurately predict antibody-antigen complex structures and conduct structure-based antibody design, which are crucial for biotherapeutics, immunity, and vaccines. By assembling a non-redundant set of test cases for antibody-antigen docking and affinity prediction, this research provides insights into the determinants of antibody recognition and molecular flexibility, showcasing the challenges faced in this diverse set of cases.
Review
Biochemistry & Molecular Biology
Stephanie Baah et al.
Summary: ADCs are a family of targeted therapeutic agents for cancer treatment, with over 80 currently in clinical development and 11 approved by the FDA. They offer enhanced targeting of cancer cells and reduced toxic side effects compared to traditional approaches, making them an attractive prospect in oncology research.
Article
Multidisciplinary Sciences
Alexander Rives et al.
Summary: The deep contextual language model trained through unsupervised learning on protein sequences contains information about biological properties, has a multiscale structural organization, and can be used to improve predictions for protein mutational effects, secondary structure, and long-range contacts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Davide Corti et al.
Summary: Monoclonal antibodies have revolutionized the treatment of several human diseases, including cancer, autoimmunity, and infectious diseases. Lessons learned from the COVID-19 pandemic have paved the way for the development of more monoclonal antibody-based therapeutics.
Article
Multidisciplinary Sciences
John Jumper et al.
Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.
Review
Immunology
Peter C. Taylor et al.
Summary: The study discusses the clinical utility of neutralizing monoclonal antibody therapies targeting SARS-CoV-2, emphasizing the importance of patient stratification, biomarkers, risk factors, and other clinical considerations.
NATURE REVIEWS IMMUNOLOGY
(2021)
Review
Chemistry, Medicinal
Yoann Le Basle et al.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2020)
Review
Biochemistry & Molecular Biology
Sara Ponziani et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Urology & Nephrology
Federica Rascio et al.
CLINICAL JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2020)
Review
Biochemistry & Molecular Biology
Umbreen Hafeez et al.
Review
Cell Biology
Ruei-Min Lu et al.
JOURNAL OF BIOMEDICAL SCIENCE
(2020)
Article
Biochemical Research Methods
Justina Jankauskaite et al.
Article
Biochemical Research Methods
Muhao Chen et al.
Article
Oncology
Virginia Bayer
SEMINARS IN ONCOLOGY NURSING
(2019)
Article
Biochemistry & Molecular Biology
Sara El-Gebali et al.
NUCLEIC ACIDS RESEARCH
(2019)
Review
Pharmacology & Pharmacy
Maria Sofia Castelli et al.
PHARMACOLOGY RESEARCH & PERSPECTIVES
(2019)
Article
Biochemistry & Molecular Biology
Raffaele Raucci et al.
Article
Immunology
Aleksandr Kovaltsuk et al.
JOURNAL OF IMMUNOLOGY
(2018)
Editorial Material
Biochemical Research Methods
Emily E. Wilton et al.
ACS SYNTHETIC BIOLOGY
(2018)
Article
Biochemical Research Methods
Francesca Nadalin et al.
Article
Biochemistry & Molecular Biology
Sarah Sirin et al.
Article
Biochemical Research Methods
Li C. Xue et al.
Article
Biology
Anna Vangone et al.
Article
Biochemical Research Methods
Iain H. Moal et al.
Article
Biochemical Research Methods
Iain H. Moal et al.
Article
Biochemistry & Molecular Biology
Panagiotis L. Kastritis et al.
Article
Biochemical Research Methods
Peter J. A. Cock et al.
Article
Chemistry, Medicinal
RX Wang et al.
JOURNAL OF MEDICINAL CHEMISTRY
(2004)
Article
Biochemistry & Molecular Biology
HM Berman et al.
NUCLEIC ACIDS RESEARCH
(2000)
