OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.

An Online tool for Fragment-based Molecule Parametrization (OFraMP) is described. OFraMP is a web application for assigning atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the Automated Topology Builder (ATB, atb.uq.

Systematic evaluation of particle loss during handling in the percutaneous transluminal angioplasty for eight different drug-coated balloons.

Paclitaxel drug coated balloons (DCBs) should provide optimal drug transfer exclusively to the target tissue. The aim of this study was to evaluate the particle loss by handling during angioplasty. A robotic arm was developed for systematic and reproducible drug abrasion experiments.

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.

A key factor in computational drug design is the consistency and reliability with which intermolecular interactions between a wide variety of molecules can be described. Here we present a procedure to efficiently, reliably and automatically assign partial atomic charges to atoms based on known distributions. We formally introduce the molecular charge assignment problem, where the task is to select a charge from a set of candidate charges for every atom of a given query molecule.

Exploring the Limits of the Geometric Copolymerization Model.

The geometric copolymerization model is a recently introduced statistical Markov chain model. Here, we investigate its practicality. First, several approaches to identify the optimal model parameters from observed copolymer fingerprints are evaluated using Monte Carlo simulated data.

New Statistical Models for Copolymerization.

For many years, copolymerization has been studied using mathematical and statistical models. Here, we present new Markov chain models for copolymerization kinetics: the Bernoulli and Geometric models. They model copolymer synthesis as a random process and are based on a basic reaction scheme.

Abundance correction for mass discrimination effects in polymer mass spectra.

Rationale: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is frequently used to analyze homo- and copolymers, i.e. for computing copolymer fingerprints.

COCONUT—An Efficient Tool for Estimating Copolymer Compositions from Mass Spectra.

The accurate characterization of synthetic polymer sequences represents a major challenge in polymer science. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is frequently used for the characterization of copolymer samples. We present the COCONUT software for estimating the composition distribution of the copolymer.