Search filters

List of works by Vytautas Gapsys

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

scientific article published on 01 January 2019

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

scientific article published on 28 April 2016

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.

scientific article published on 10 November 2017

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase

scientific article

Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

scientific article published in 2022

Calculation of binding free energies

scientific article published in January 2015

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

scientific article published on 20 June 2019

Computational analysis of local membrane properties

scientific article

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

article

Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations.

scientific article

GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design

scientific article published on 30 March 2022

Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings.

scientific article

Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.

scientific article published on 31 August 2016

Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization

scientific article (publication date: 2011)

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

scientific article published on 06 June 2012

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors

scientific article published on 19 May 2020

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

scientific article published on 24 November 2020

On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

scientific article published on 19 August 2020

Optimal Superpositioning of Flexible Molecule Ensembles ⬇️

scientific article published on January 8, 2013

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

scientific article published on 01 November 2019

Phosphorylation drives a dynamic switch in serine/arginine-rich proteins

scientific article published on 31 October 2013

Polycation-Anionic Lipid Membrane Interactions

scientific article published on 15 October 2020

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

scientific article published in 2022

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

scientific article published on 13 August 2019

Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

scientific article published on 30 May 2022

Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation

scientific article published on 13 April 2019

Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation

scientific article

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

scientific article published on 22 October 2015

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

scientific article published on 27 January 2020

Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets

scientific article published on 12 April 2018

pmx Webserver: A User Friendly Interface for Alchemistry.

scientific article

pmx: Automated protein structure and topology generation for alchemical perturbations.

scientific article

Paulina is supported by:

About Paulina

Help