Related papers: PIPER: An FFT-based Protein Docking Program with P…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Foundation models (FMs) have shown prominent success in a wide range of tasks. Their applicability to specific domain-task pairings relies on the availability of, both, high-quality data and significant computational resources. These…
Density functional theory (DFT), the most widely adopted method in modern computational chemistry, fails to describe accurately the electronic structure of strongly correlated systems. Here we show that DFT can be formally and practically…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
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…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…
Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…
The Fast Fourier Transform(FFT) is a classic signal processing algorithm that is utilized in a wide range of applications. For image processing, FFT computes on every pixel's value of an image, regardless of their properties in frequency…
Pair atomic density fitting (PADF) is a promising strategy to reduce the scaling with system size of quantum chemical methods for the calculation of the correlation energy like the direct random phase approximation (RPA) or second-order…
We propose a Fast Fourier Transform based Periodic Interpolation Method (FFT-PIM), a flexible and computationally efficient approach for computing the scalar potential given by a superposition sum in a unit cell of an infinitely periodic…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
With tens of petaflops supercomputers already in operation and exaflops machines expected to appear within the next 10 years, efficient parallel computational methods are required to take advantage of such extreme-scale machines. In this…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
Protein interactions and assembly formation are fundamental to most biological processes. Predicting the assembly structure from constituent proteins -- referred to as the protein docking task -- is thus a crucial step in protein design…
Density-potential functional theory (DPFT) is an alternative formulation of orbital-free density functional theory that may be suitable for modeling the electronic structure of large systems. To date, DPFT has been applied mainly to quantum…
Efficiently recovering dynamic correlation in strongly correlated systems without incurring prohibitive computational costs remains a central challenge in quantum chemistry. In this Perspective, we review and benchmark methods capable of…
A combined density and first-order reduced-density-matrix (1RDM) functional method is proposed for the calculation of potential energy curves (PECs) of molecular multibond dissociation. Its 1RDM functional part, a pair density functional,…