Modulators of protein–protein interactions
LG Milroy, TN Grossmann, S Hennig… - Chemical …, 2014 - ACS Publications
Since Hedin's characterization of trypsin and antitrypsin in 1906,(1) arguably the first
account of a regulatory protein–protein interaction (PPI), contemporary understanding of …
account of a regulatory protein–protein interaction (PPI), contemporary understanding of …
Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?
C Rakers, M Bermudez, BG Keller… - Wiley …, 2015 - Wiley Online Library
As an essential part of many biological processes, protein–protein interactions (PPIs) offer
exciting and promising opportunities for drug discovery by extension of the druggable target …
exciting and promising opportunities for drug discovery by extension of the druggable target …
MDverse: shedding light on the dark matter of molecular dynamics simulations
JKS Tiemann, M Szczuka, L Bouarroudj, M Oussaren… - bioRxiv, 2023 - biorxiv.org
The rise of open science and the absence of a global dedicated data repository for
molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist …
molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist …
Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis
S Gu, DA Silva, L Meng, A Yue… - PLoS computational …, 2014 - journals.plos.org
Protein-ligand recognition plays key roles in many biological processes. One of the most
fascinating questions about protein-ligand recognition is to understand its underlying …
fascinating questions about protein-ligand recognition is to understand its underlying …
Small‐Molecule Proteomimetic Inhibitors of the HIF‐1α–p300 Protein–Protein Interaction
The therapeutically relevant hypoxia inducible factor HIF‐1α–p300 protein–protein
interaction can be orthosterically inhibited with α‐helix mimetics based on an oligoamide …
interaction can be orthosterically inhibited with α‐helix mimetics based on an oligoamide …
Molecular simulation of conformational pre-organization in cyclic RGD peptides
To test the ability of molecular simulations to accurately predict the solution-state
conformational properties of peptidomimetics, we examined a test set of 18 cyclic RGD …
conformational properties of peptidomimetics, we examined a test set of 18 cyclic RGD …
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics
GA Pantelopulos, S Mukherjee… - … : Structure, Function, and …, 2015 - Wiley Online Library
The p53‐MDM2 complex is both a major target for cancer drug development and a valuable
model system for computational predictions of protein‐ligand binding. To investigate the …
model system for computational predictions of protein‐ligand binding. To investigate the …
Cystobactamids 920-1 and 920-2: Assignment of the Constitution and Relative Configuration by Total Synthesis
T Planke, M Moreno, S Hüttel, J Fohrer, F Gille… - Organic …, 2019 - ACS Publications
Total synthesis of cystobactamid 920-1 and its epimer has allowed an unambiguous
assignment of the relative and absolute configuration of the natural product. A careful …
assignment of the relative and absolute configuration of the natural product. A careful …
Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)
Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide
polyamides) can be referred to as minimalist mimics. Accessible conformations of these …
polyamides) can be referred to as minimalist mimics. Accessible conformations of these …
Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking
MDM2 is a negative regulator of p53 activity and an important target for cancer therapeutics.
The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its …
The N-terminal lid region of MDM2 modulates interactions with p53 via competition for its …