BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK

(2013) Michael Zahn et al.   JOURNAL OF MOLECULAR BIOLOGY

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Conformational Selection in Substrate Recognition by Hsp70 Chaperones

(2012) Moritz Marcinowski et al.   JOURNAL OF MOLECULAR BIOLOGY

The diverse members of the mammalian HSP70 machine show distinct chaperone-like activities

(2011) Jurre Hageman et al.   BIOCHEMICAL JOURNAL

Substrate discrimination of the chaperone BiP by autonomous and cochaperone-regulated conformational transitions

(2011) Moritz Marcinowski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Predicting MHC class I epitopes in large datasets

(2010) Kirsten Roomp et al.   BMC BIOINFORMATICS

Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate

(2009) E. B. Bertelsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

(2009) Joost Van Durme et al.   PLoS Computational Biology

Allosteric Coupling between the Lid and Interdomain Linker in DnaK Revealed by Inhibitor Binding Studies

(2008) M. Liebscher et al.   JOURNAL OF BACTERIOLOGY

Docking and scoring with alternative side-chain conformations

(2008) Christoph Hartmann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS