虽然基于x射线的方法是迄今为止最突出的,但基于核磁共振(NMR)和基于电子显微镜(EM)的方法也很有特色。例如蛋白质数据库(PDB),一个蛋白质3D结构的数据库,包括近90%的用x射线晶体学解析的结构(如果只考虑已知配体-蛋白质结合亲和力的结构,则几乎是99%)和近8%的用NMR解析的结构。有关方法和统计数据的信息可以在PDB...
data-sciencebioinformaticsaicancerprotein-structurecomputational-biologyhigh-performance-computingdrug-discoveryantibodydrug-designoncologypd-1protein-dockingantibody-designprotien-foldingprotein-diffusionevodiff UpdatedJul 31, 2024 Shell OPUS-Fold3: a gradient-based protein all-atom folding and docking framework ...
Protein-docking is a molecular modeling problem which aims to predict, with computer science algorithms and techniques, the mutual orientation and position of two molecules forming a complex. From: Encyclopedia of Bioinformatics and Computational Biology, 2019 ...
AlphaFold2Protein-ligand dockingStructure-based virtual screeningStructure-based virtual screening (SBVS) is a crucial computational approach in drug discovery, ... J Song,J Ha,J Lee,... - 《Scientific Reports》 被引量: 0发表: 2024年 Structure comparison of heme-binding sites in heme protein ...
可以预测docking构象,同时还额外的可以预测结合的亲和力大小 不直接预测构象,而是先预测一个contact map,再根据它来预测结合构象 总结 受到alphafold2的启发,引入了三角约束 充分利用局部功能区(在生物学上一般会更加保守,且和结合很相关): 1) 三角约束里会用 2) 设计对比损失函数时会用 建模了两种先验: 三角约束先...
Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming...
An alternative approach to experimental structure determination is to use computational modelling methods. These approaches, such as structure prediction from sequence or protein-protein docking, can also provide insight into atomistic details of biomolecules but are frequently limited in accuracy due to th...
AI-Bind is a deep-learning pipeline that provides interpretable binding predictions for never-before-seen proteins and ligands. AI-Bind is capable of rapid screening of large chemical libraries and guiding computationally expensive auto-docking simulations by prioritizing protein-ligand pairs for validation...
Molecular docking plays a significant role in early-stage drug discovery, from structure-based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive power is critically dependent on the protein–ligand scoring function. In this review, we give a broad overview of ...
Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming...