Common dictionaries in behavioral research.

Common dictionaries in behavioral research.</p

Empirical results of top 15 opinionated terms in movie reviews.

Empirical results of top 15 opinionated terms in movie reviews.</p

SLICK − Scoring and Energy Functions for Protein−Carbohydrate Interactions

Protein−carbohydrate interactions are increasingly being recognized as essential for many important biomolecular recognition processes. From these, numerous biomedical applications arise in areas as diverse as drug design, immunology, or drug transport. We introduce SLICK, a package containing a scoring and an energy function, which were specifically designed to predict binding modes and free energies of sugars and sugarlike compounds to proteins. SLICK accounts for van der Waals interactions, solvation effects, electrostatics, hydrogen bonds, and CH···π interactions, the latter being a particular feature of most protein−carbohydrate interactions. Parameters for the empirical energy function were calibrated on a set of high-resolution crystal structures of protein−sugar complexes with known experimental binding free energies. We show that SLICK predicts the binding free energies of predicted complexes (through molecular docking) with high accuracy. SLICK is available as part of our molecular modeling package BALL (www.ball-project.org)

Summary statistics of statistical inferences with word tuples.

Summary statistics of statistical inferences with word tuples.</p

Summary statistics for hypothesis testing with movie reviews.

Summary statistics for hypothesis testing with movie reviews.</p

Comparison of human classifications to statistical inferences.

Comparison of human classifications to statistical inferences.</p

Empirical results of top 15 polarity expressions in financial filings.

Empirical results of top 15 polarity expressions in financial filings.</p

A Fully Computational Model for Predicting Percutaneous Drug Absorption

The prediction of transdermal absorption for arbitrary penetrant structures has several important applications in the pharmaceutical industry. We propose a new data-driven, predictive model for skin permeability coefficients kp based on an ensemble model using k-nearest-neighbor models and ridge regression. The model was trained and validated with a newly assembled data set containing experimental data and structures for 110 compounds. On the basis of three purely computational descriptors (molecular weight, calculated octanol/water partition coefficient, and solvation free energy), we have developed a model allowing for the reliable, purely computational prediction of skin permeability coefficients. The model is both accurate and robust, as we showed in an extensive validation (correlation coefficient for leave-one-out cross validation:  Q = 0.948, mean standard error:  0.2 for log kp)

BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking

Protein−ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies

GERFWF_Alignment_1056

This alignment comprises 1056 DNA barcodes belonging to 93 species of freshwater fishes and lampreys from Germany