Beyond Tripeptides Two-Step Active Machine Learning for Very Large Data sets

Injectable self-assembled bola-dipeptide hydrogels for sustained photodynamic prodrug delivery and enhanced tumor therapy

(2020) Qianli Zou et al.   JOURNAL OF CONTROLLED RELEASE

On active learning methods for manifold data

(2020) Hang Li et al.   TEST

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

(2020) Kirill Shmilovich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale computational prediction of β-sheet peptide self-assembly morphology

(2020) Li Deng et al.   MOLECULAR SIMULATION

Design of self-assembly dipeptide hydrogels and machine learning via their chemical features

(2019) Fei Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strategy to Identify Improved N-Terminal Modifications for Supramolecular Phenylalanine-Derived Hydrogelators

(2019) Brittany L. Abraham et al.   LANGMUIR

Induction of p73, Δ133p53, Δ160p53, pAKT lead to neuroprotection via DNA repair by 5-LOX inhibition

(2019) Shashank Shekhar et al.   MOLECULAR BIOLOGY REPORTS

DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity

(2019) Jingcheng Wu et al.   Frontiers in Immunology

Effect of self-assembly on antimicrobial activity of double-chain short cationic lipopeptides

(2019) Oktawian Stachurski et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Can machine learning find extraordinary materials?

(2019) Steven K. Kauwe et al.   COMPUTATIONAL MATERIALS SCIENCE

Toward insights on determining factors for high activity in antimicrobial peptides via machine learning

(2019) Hao Li et al.   PeerJ

Guiding principles for peptide nanotechnology through directed discovery

(2018) A. Lampel et al.   CHEMICAL SOCIETY REVIEWS

Designing Anticancer Peptides by Constructive Machine Learning

(2018) Francesca Grisoni et al.   ChemMedChem

Machine-Learning-Based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency with Improved Accuracy

(2018) Balachandran Manavalan et al.   JOURNAL OF PROTEOME RESEARCH

Experimental search for high-temperature ferroelectric perovskites guided by two-step machine learning

(2018) Prasanna V. Balachandran et al.   Nature Communications

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

(2018) Jie Dong et al.   Journal of Cheminformatics

Mordred: a molecular descriptor calculator

(2018) Hirotomo Moriwaki et al.   Journal of Cheminformatics

The greening of peptide synthesis

(2017) Stefan B. Lawrenson et al.   GREEN CHEMISTRY

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

Mapping membrane activity in undiscovered peptide sequence space using machine learning

(2016) Ernest Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical self-assembly of di-, tri- and tetraphenylalanine peptides capped with two fluorenyl functionalities: from polymorphs to dendrites

(2016) Enric Mayans et al.   Soft Matter

Will it gel? Successful computational prediction of peptide gelators using physicochemical properties and molecular fingerprints

(2016) Jyoti K. Gupta et al.   Chemical Science

The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation

(2016) Lijun Liang et al.   RSC Advances

Tetrapeptide unfolding dynamics followed by core-level spectroscopy: a first-principles approach

(2015) Simone Taioli et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays

(2014) Frédérique Deiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

(2014) Pim W. J. M. Frederix et al.   Nature Chemistry

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

(2011) Pim W. J. M. Frederix et al.   Journal of Physical Chemistry Letters

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae

(2010) Andrea F. Moon et al.   NUCLEIC ACIDS RESEARCH

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

(2009) Alexander Stukowski   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Keratocyte behavior in three-dimensional photopolymerizable poly(ethylene glycol) hydrogels

(2008) Nerea Garagorri et al.   Acta Biomaterialia

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation

Sequence shuffle controls morphological consequences in a self-assembling tetrapeptide

(2007) K. B. Joshi et al.   JOURNAL OF PEPTIDE SCIENCE