Leopard syndrome: a report of five cases from one family in two generations.

Unlabelled: This is the first reported family with Leopard syndrome (LS) from Bosnia and Herzegovina. We report five cases of LS from two generations of the same family. In the present series of patients from one family, all patients carry the same recurrent mutation Y279C in the PTPN11 gene, exhibiting different phenotypes and a variable expression of multiple lentigines.

Confidence-guided local structure prediction with HHfrag.

We present a method to assess the reliability of local structure prediction from sequence. We introduce a greedy algorithm for filtering and enrichment of dynamic fragment libraries, compiled with remote-homology detection methods such as HHfrag. After filtering false hits at each target position, we reduce the fragment library to a minimal set of representative fragments, which are guaranteed to have correct local structure in regions of detectable conservation.

CSB: a Python framework for structural bioinformatics.

Summary: Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice.

Availability: Stable release packages are available for download from the Python Package Index (PyPI) as well as from the project's website http://csb.

A Boy with Holt-Oram Syndrome Caused by Novel Mutation c.1304delT in the TBX5 Gene.

Holt-Oram syndrome (HOS) is an autosomal dominant developmental defect involving preaxial radial ray upper limb deformity and variable cardiac defects. It has been demonstrated that HOS is caused by mutations in the T-box transcription factor gene TBX5. Numerous germline mutations (more than 60) of this gene produce preterminal stop codons, which lead to synthesis of a truncated nonfunctional TBX5 protein.

HHfrag: HMM-based fragment detection using HHpred.

Motivation: Over the last decade, both static and dynamic fragment libraries for protein structure prediction have been introduced. The former are built from clusters in either sequence or structure space and aim to extract a universal structural alphabet. The latter are tailored for a particular query protein sequence and aim to provide local structural templates that need to be assembled in order to build the full-length structure.