Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein-ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein-ligand interaction landscape, which will be explored in further applications.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767528 | PMC |
| http://dx.doi.org/10.1007/s10822-017-0069-7 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Effects of Age on the Bone-Conduction Amplitude-Modulated cVEMP Temporal Modulation Transfer Function.
Ear Hear
December 2024
Department of Communication Sciences and Disorders, James Madison University, Harrisonburg, Virginia, USA.
Objectives: Cervical vestibular evoked myogenic potentials (cVEMPs) reflect saccular stimulation that results in an inhibitory muscle reflex recorded over the sternocleidomastoid muscle. These responses are utilized to study basic vestibular functions and are also applied clinically. Traditionally, cVEMPs have utilized transient stimuli such as clicks and tonebursts to evoke onset responses.
View Article and Find Full Text PDF3D deuterium metabolic imaging (DMI) of the human liver at 7 T using low-rank and subspace model-based reconstruction.
Magn Reson Med
December 2024
Center for Image Sciences, High Field MR Research Group, Department of Radiology, University Medical Centre Utrecht, Utrecht, The Netherlands.
Purpose: To implement a low-rank and subspace model-based reconstruction for 3D deuterium metabolic imaging (DMI) and compare its performance against Fourier transform-based (FFT) reconstruction in terms of spectral fitting reliability.
Methods: Both reconstruction methods were applied on simulated and experimental DMI data. Numerical simulations were performed to evaluate the effect of increasing acceleration factors.
A fully linearized ADMM algorithm for optimization based image reconstruction.
J Xray Sci Technol
December 2024
Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA.
Background And Objective: Optimization based image reconstruction algorithm is an advanced algorithm in medical imaging. However, the corresponding solving algorithm is challenging because the model is usually large-scale and non-smooth. This work aims to devise a simple and convergent solver for optimization model.
View Article and Find Full Text PDFSPECTRAL BRAIN GRAPH NEURAL NETWORK FOR PREDICTION OF ANXIETY IN CHILDREN WITH AUTISM SPECTRUM DISORDER.
Proc IEEE Int Symp Biomed Imaging
May 2024
Department of Biomedical Engineering, Yale University, USA.
Children with Autism Spectrum Disorder (ASD) frequently exhibit comorbid anxiety, which contributes to impairment and requires treatment. Therefore, it is critical to investigate co-occurring autism and anxiety with functional imaging tools to understand the brain mechanisms of this comorbidity. Multidimensional Anxiety Scale for Children, 2nd edition (MASC-2) score is a common tool to evaluate the daily anxiety level in autistic children.
View Article and Find Full Text PDFOne Receptor Show: Evaluation of Feature Extraction Methods for a Single Gas Sensor Based on α-Tocopherol-Substituted Zinc Phthalocyanine.
ACS Sens
December 2024
Tor Vergata University of Rome, Department of Chemical Sciences and Technologies, Rome 00133, Italy.
A consistent part of gas sensor research activities aims to improve sensing performances by synthesizing new sensing materials, improving the selection of elements in arrays, and optimizing the feature extraction and classification algorithms. This paper combines most of these aspects to confer selectivity to a low-selectivity sensor by using feature extraction algorithms applied to the sensor response kinetics. Several algorithms were employed to represent the kinetic behavior of the sensor response during the adsorption and desorption phases.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!