Latest Articles of Journal of Chemical Information and Modeling


Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations 10.1021/acs.jcim.7b00663 2018-03-07 Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual parametrization ...
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds 10.1021/acs.jcim.7b00496 2018-03-06 The MolFind application has been developed as a nontargeted metabolomics chemometric tool to facilitate structure identification when HPLC biofluids analysis reveals a feature of interest. Here synthetic compounds are selected and measured to form the basis o...
Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets 10.1021/acs.jcim.7b00733 2018-03-06 Saturation transfer difference (STD) is an NMR technique conventionally applied in drug discovery to identify ligand moieties relevant for binding to protein cavities. This is important to direct medicinal chemistry efforts in small-molecule optimization proc...
Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods 10.1021/acs.jcim.7b00642 2018-03-05 Water molecules play an important role in the association of drugs with their pharmaceutical targets. For this reason, calculating the energetic contribution of water is essential to make accurate predictions of compounds’ affinity and selectivity. Water mole...
Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex 10.1021/acs.jcim.7b00636 2018-03-02 DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event t...
Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors 10.1021/acs.jcim.7b00625 2018-03-01 Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein–ligand efficiency interactions that can later be g...
TCMAnalyzer: A Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine 10.1021/acs.jcim.7b00549 2018-03-01 Traditional Chinese medicine (TCM) has been widely used and proven effective in long term clinical practice. However, the molecular mechanism of action for many TCMs remains unclear due to the complexity of many ingredients and their interactions with biologi...
Optimal HTS Fingerprint Definitions by Using a Desirability Function and a Genetic Algorithm 10.1021/acs.jcim.7b00447 2018-02-22 The use of compound biological fingerprints built on data from high-throughput screening (HTS) campaigns, or HTS fingerprints, is a novel cheminformatics method of representing compounds by integrating chemical and biological activity data that is gaining mom...
New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures 10.1021/acs.jcim.7b00601 2018-02-22 Accurate prediction of a protein’s structure requires a reliable free energy function that consists of both enthalpic and entropic contributions. Although considerable progresses have been made in the calculation of potential energies in protein structure pre...
Assessment and Reproducibility of Quantitative Structure–Activity Relationship Models by the Nonexpert 10.1021/acs.jcim.7b00523 2018-02-22 Model reliability is generally assessed and reported as an intrinsic component of quantitative structure–activity relationship (QSAR) publications; it can be evaluated using defined quality criteria such as the Organisation for Economic Cooperation and Develo...

Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations

10.1021/acs.jcim.7b00663

2018-03-07

Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual parametrization ...

Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds

10.1021/acs.jcim.7b00496

2018-03-06

The MolFind application has been developed as a nontargeted metabolomics chemometric tool to facilitate structure identification when HPLC biofluids analysis reveals a feature of interest. Here synthetic compounds are selected and measured to form the basis o...

Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets

10.1021/acs.jcim.7b00733

2018-03-06

Saturation transfer difference (STD) is an NMR technique conventionally applied in drug discovery to identify ligand moieties relevant for binding to protein cavities. This is important to direct medicinal chemistry efforts in small-molecule optimization proc...

Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods

10.1021/acs.jcim.7b00642

2018-03-05

Water molecules play an important role in the association of drugs with their pharmaceutical targets. For this reason, calculating the energetic contribution of water is essential to make accurate predictions of compounds’ affinity and selectivity. Water mole...

Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex

10.1021/acs.jcim.7b00636

2018-03-02

DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event t...

Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors

10.1021/acs.jcim.7b00625

2018-03-01

Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein–ligand efficiency interactions that can later be g...

TCMAnalyzer: A Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine

10.1021/acs.jcim.7b00549

2018-03-01

Traditional Chinese medicine (TCM) has been widely used and proven effective in long term clinical practice. However, the molecular mechanism of action for many TCMs remains unclear due to the complexity of many ingredients and their interactions with biologi...

Optimal HTS Fingerprint Definitions by Using a Desirability Function and a Genetic Algorithm

10.1021/acs.jcim.7b00447

2018-02-22

The use of compound biological fingerprints built on data from high-throughput screening (HTS) campaigns, or HTS fingerprints, is a novel cheminformatics method of representing compounds by integrating chemical and biological activity data that is gaining mom...

New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures

10.1021/acs.jcim.7b00601

2018-02-22

Accurate prediction of a protein’s structure requires a reliable free energy function that consists of both enthalpic and entropic contributions. Although considerable progresses have been made in the calculation of potential energies in protein structure pre...

Assessment and Reproducibility of Quantitative Structure–Activity Relationship Models by the Nonexpert

10.1021/acs.jcim.7b00523

2018-02-22

Model reliability is generally assessed and reported as an intrinsic component of quantitative structure–activity relationship (QSAR) publications; it can be evaluated using defined quality criteria such as the Organisation for Economic Cooperation and Develo...