Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
Rauscher, Sarah, Gapsys, Vytautas, Gajda, Michal J, Zweckstetter, Markus, de Groot, Bert L, Grubmüller, Helmut
Published in Journal of chemical theory and computation (10.11.2015)
Published in Journal of chemical theory and computation (10.11.2015)
Get full text
Journal Article
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
Rizzi, Andrea, Jensen, Travis, Slochower, David R., Aldeghi, Matteo, Gapsys, Vytautas, Ntekoumes, Dimitris, Bosisio, Stefano, Papadourakis, Michail, Henriksen, Niel M., de Groot, Bert L., Cournia, Zoe, Dickson, Alex, Michel, Julien, Gilson, Michael K., Shirts, Michael R., Mobley, David L., Chodera, John D.
Published in Journal of computer-aided molecular design (01.05.2020)
Published in Journal of computer-aided molecular design (01.05.2020)
Get full text
Journal Article
A litmus test for classifying recognition mechanisms of transiently binding proteins
Chakrabarti, Kalyan S., Olsson, Simon, Pratihar, Supriya, Giller, Karin, Overkamp, Kerstin, Lee, Ko On, Gapsys, Vytautas, Ryu, Kyoung-Seok, de Groot, Bert L., Noé, Frank, Becker, Stefan, Lee, Donghan, Weikl, Thomas R., Griesinger, Christian
Published in Nature communications (01.07.2022)
Published in Nature communications (01.07.2022)
Get full text
Journal Article
Consistent Prediction of Mutation Effect on Drug Binding in HIV‑1 Protease Using Alchemical Calculations
Bastys, Tomas, Gapsys, Vytautas, Doncheva, Nadezhda T, Kaiser, Rolf, de Groot, Bert L, Kalinina, Olga V
Published in Journal of chemical theory and computation (10.07.2018)
Published in Journal of chemical theory and computation (10.07.2018)
Get full text
Journal Article
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors
Bastys, Tomas, Gapsys, Vytautas, Walter, Hauke, Heger, Eva, Doncheva, Nadezhda T, Kaiser, Rolf, de Groot, Bert L, Kalinina, Olga V
Published in Retrovirology (19.05.2020)
Published in Retrovirology (19.05.2020)
Get full text
Journal Article
Automated relative binding free energy calculations from SMILES to ΔΔG
Moore, J. Harry, Margreitter, Christian, Janet, Jon Paul, Engkvist, Ola, de Groot, Bert L., Gapsys, Vytautas
Published in Communications chemistry (27.04.2023)
Published in Communications chemistry (27.04.2023)
Get full text
Journal Article
Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization
Matthes, Dirk, Gapsys, Vytautas, Daebel, Venita, de Groot, Bert L
Published in PloS one (03.05.2011)
Published in PloS one (03.05.2011)
Get full text
Journal Article
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes
Gapsys, Vytautas, de Groot, Bert L
Published in Journal of chemical theory and computation (12.12.2017)
Published in Journal of chemical theory and computation (12.12.2017)
Get full text
Journal Article
Chemical Space Exploration with Active Learning and Alchemical Free Energies
Khalak, Yuriy, Tresadern, Gary, Hahn, David F., de Groot, Bert L., Gapsys, Vytautas
Published in Journal of chemical theory and computation (11.10.2022)
Published in Journal of chemical theory and computation (11.10.2022)
Get full text
Journal Article
Biomolecular simulations at the exascale: From drug design to organelles and beyond
Gapsys, Vytautas, Kopec, Wojciech, Matthes, Dirk, de Groot, Bert L.
Published in Current opinion in structural biology (01.10.2024)
Published in Current opinion in structural biology (01.10.2024)
Get full text
Journal Article