Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

(2018) Baudoin Delépine et al.   METABOLIC ENGINEERING

VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening

(2017) José-Manuel Gally et al.   Molecular Informatics

Computer-Assisted Synthetic Planning: The End of the Beginning

(2016) Sara Szymkuć et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Reaction Decoder Tool (RDT): extracting features from chemical reactions

(2016) Syed Asad Rahman et al.   BIOINFORMATICS

Faster Algorithms for Isomer Network Generation

(2016) Dheivya Thiagarajan et al.   Journal of Chemical Information and Modeling

Semisupervised Gaussian Process for Automated Enzyme Search

(2016) Joseph Mellor et al.   ACS Synthetic Biology

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

(2016) Noushin Hadadi et al.   ACS Synthetic Biology

DynaMet: A Fully Automated Pipeline for Dynamic LC–MS Data

(2015) Patrick Kiefer et al.   ANALYTICAL CHEMISTRY

De Novo Fragment Design for Drug Discovery and Chemical Biology

(2015) Tiago Rodrigues et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering

(2014) Tamás Fehér et al.   Biotechnology Journal

Future De Novo Drug Design

(2014) Gisbert Schneider   Molecular Informatics

A Short Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility

(2014) Wendy A. Warr   Molecular Informatics

XTMS: pathway design in an eXTended metabolic space

(2014) Pablo Carbonell et al.   NUCLEIC ACIDS RESEARCH

Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

(2014) Mengjin Liu et al.   PLoS One

Molpher: a software framework for systematic chemical space exploration

(2014) David Hoksza et al.   Journal of Cheminformatics

De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach

(2013) Kentaro Kawai et al.   Journal of Chemical Information and Modeling

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

(2013) Aaron M. Virshup et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library

(2013) Hannes L. Röst et al.   PROTEOMICS

Lattice Enumeration for Inverse Molecular Design Using the Signature Descriptor

(2012) Shawn Martin   Journal of Chemical Information and Modeling

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

OMG: Open Molecule Generator

(2012) Julio E Peironcely et al.   Journal of Cheminformatics

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

Natural Product-Like Virtual Libraries: Recursive Atom-Based Enumeration

(2011) Melvin J. Yu   Journal of Chemical Information and Modeling

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

Search for Novel Aminoglycosides by Combining Fragment-Based Virtual Screening and 3D-QSAR Scoring

(2009) Piotr Setny et al.   Journal of Chemical Information and Modeling