相关论文: CABS-dock web server for the flexible docking of p…

The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their…

We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have…

Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in…

Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance…

Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…

Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…

The ABC (ATP Binding Cassette) transporter protein superfamily comprises a large number of ubiquitous and functionally versatile proteins conserved from archaea to humans. ABC transporters have a key role in many human diseases and also in…

Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…

Molecular docking, given a ligand molecule and a ligand binding site (called ``pocket'') on a protein, predicting the binding mode of the protein-ligand complex, is a widely used technique in drug design. Many deep learning models have been…

Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large…

Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as…

Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…

We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…

The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate…

Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…

Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not…

Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…

Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…