Vojtěch Spiwok
YOU?
Author Swipe
View article: Allosteric Inhibitors of SARS‐CoV‐2 RNA‐Dependent RNA Polymerase Based on <i>N</i> , <i>N′</i> ‐Diphenylurea
Allosteric Inhibitors of SARS‐CoV‐2 RNA‐Dependent RNA Polymerase Based on <i>N</i> , <i>N′</i> ‐Diphenylurea Open
The COVID‐19 pandemic, caused by the highly transmissible SARS‐CoV‐2 virus, has highlighted the urgent need for effective small‐molecule antivirals. To date, only a few such agents, including molnupiravir and remdesivir, have been approved…
View article: Design of proteins by parallel tempering in the sequence space
Design of proteins by parallel tempering in the sequence space Open
Computational design of new proteins is often performed by optimizing the amino acid sequence. This sequence is characterized by an energy (lower energy means better propensity to form the desired 3D structure) that is sampled and minimize…
View article: Design of proteins by parallel tempering in the sequence space
Design of proteins by parallel tempering in the sequence space Open
Design of new proteins is often formulated as an optimization task. An amino acid sequence is characterized by an energy, and this energy is sampled and minimized. Here, we use a parallel tempering algorithm to accelerate this task. A seri…
View article: PLUMED Tutorials: A collaborative, community-driven learning ecosystem
PLUMED Tutorials: A collaborative, community-driven learning ecosystem Open
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users pre…
View article: PLUMED Tutorials: a collaborative, community-driven learning ecosystem
PLUMED Tutorials: a collaborative, community-driven learning ecosystem Open
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users p…
View article: CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein Open
The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE challenge in which 23 computational teams each select…
View article: Analysis of metadynamics simulations by metadynminer.py
Analysis of metadynamics simulations by metadynminer.py Open
Motivation Molecular dynamics simulation is very useful but computationally demanding method of studying dynamics of biomolecular systems. Many enhanced sampling methods were developed in order to obtain the desired results in available co…
View article: Developing Allosteric Inhibitors of SARS‐CoV‐2 RNA‐Dependent RNA Polymerase
Developing Allosteric Inhibitors of SARS‐CoV‐2 RNA‐Dependent RNA Polymerase Open
The use of Fpocket and virtual screening techniques enabled us to identify potential allosteric druggable pockets within the SARS‐CoV‐2 RNA‐dependent RNA polymerase (RdRp). Of the compounds screened, compound 1 was identified as a promisin…
View article: CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson’s Disease associated protein
CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson’s Disease associated protein Open
The CACHE challenges are a series of prospective benchmarking exercises meant to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE #1 challenge in which 23 computational teams ea…
View article: Uncertainties of predictions from temperature replica exchange simulations
Uncertainties of predictions from temperature replica exchange simulations Open
Parallel tempering molecular dynamics simulation, also known as temperature replica exchange simulation, is a popular enhanced sampling method used to study biomolecular systems. This method makes it possible to calculate the free energy d…
View article: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics
Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics Open
The potential of molecular simulations is limited by their computational costs. There is often a need to accelerate simulations using some of the enhanced sampling methods. Metadynamics applies a history-dependent bias potential that disfa…
View article: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics - 2
Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics - 2 Open
Supplementary files (trajectories, scripts for analysis and generation of images and other data). Data for metadynamics with two parametric time-lagged tSNE collective variables are in the mtd1 directory. Data for metadynamics with two par…
View article: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics
Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics Open
Supporting information for: Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics by H. Hradiská, M. Kurečka, J. Beránek, G. Tedeschi, V. Višňovský, A. Křenek, V. Spiwok Supplementary files for the analysis by P…
View article: 2,6-Disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines as a new class of potent antitubercular agents inhibiting DprE1
2,6-Disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines as a new class of potent antitubercular agents inhibiting DprE1 Open
Phenotypic screening of an in-house library of small molecule purine derivatives against Mycobacterium tuberculosis (Mtb) led to the identification of 2-morpholino-7-(naphthalen-2-ylmethyl)-1,7-dihydro-6H-purin-6-one 10 as a potent antimyc…
View article: Hypolipidemic Activity of Sesquiterpene Lactones and their Derivatives
Hypolipidemic Activity of Sesquiterpene Lactones and their Derivatives Open
BACKGROUND: Despite the available range of lipid-lowering drugs, mainly of synthetic origin, the problem of atherosclerosis therapy and its manifestations remain unresolved. Bioinformatics methods, in particular molecular docking, are cons…
View article: Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Open
Here, we demonstrate a method to estimate the uncertainty (confidence intervals and standard errors) of free energy differences calculated by molecular simulations. The widths of confidence intervals and standard errors can be calculated s…
View article: Cytotoxicity and Antitumor Activity of Arglabin and its Derivatives
Cytotoxicity and Antitumor Activity of Arglabin and its Derivatives Open
BACKGROUND: At present, more than 8000 sesquiterpene lactones have been isolated and described from natural sources, a significant part of which has cytotoxicity and antitumor activity. One of the practically available sesquiterpene lacton…
View article: Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d
Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d Open
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realisticall…
View article: Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Open
Here we demonstrate a method to estimate the errors of free energy differences calculated by molecular simulations. The widths of the confidence intervals can be calculated solely from temperature and the number of transitions between stat…
View article: Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Open
Supporting data for Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Molecular simulations make it possible to predict equilibrium constants and corresponding free energy differences. Fo…
View article: Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Open
Supporting data for Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Molecular simulations make it possible to predict equilibrium constants and corresponding free energy differences. Fo…
View article: Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts
Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Open
Supporting data for Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Molecular simulations make it possible to predict equilibrium constants and corresponding free energy differences. Fo…
View article: Collective Variable for Metadynamics Derived From AlphaFold Output
Collective Variable for Metadynamics Derived From AlphaFold Output Open
AlphaFold is a neural network–based tool for the prediction of 3D structures of proteins. In CASP14, a blind structure prediction challenge, it performed significantly better than other competitors, making it the best available structure p…
View article: Analysis of Plumed output by Metadynminer - Plumed Masterclass 2022
Analysis of Plumed output by Metadynminer - Plumed Masterclass 2022 Open
We provide input data for the Plumed Masterclass "Analysis of Plumed output by Metadynminer". Input and output data are available for metadynamics simulations of alanine dipeptide in water using Gromacs and Plumed. It was calculated with t…
View article: Analysis of Plumed output by Metadynminer - Plumed Masterclass 2022
Analysis of Plumed output by Metadynminer - Plumed Masterclass 2022 Open
We provide input data for the Plumed Masterclass "Analysis of Plumed output by Metadynminer". Input and output data are available for metadynamics simulations of alanine dipeptide in water using Gromacs and Plumed. It was calculated with t…
View article: Collective Variable for Metadynamics Derived from AlphaFold Output
Collective Variable for Metadynamics Derived from AlphaFold Output Open
AlphaFold is the state of the art method for prediction of 3D structures of proteins from the amino acid sequence by neural networks. One of the outputs of AlphaFold is a probability profile of inter-residue distances for all residue pairs…
View article: Collective Variable for Metadynamics Derived from AlphaFold Output
Collective Variable for Metadynamics Derived from AlphaFold Output Open
AlphaFold is the state of the art method for prediction of 3D structures of proteins from the amino acid sequence by neural networks. One of the outputs of AlphaFold is a probability profile of inter-residue distances for all residue pairs…