RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structur...

One of the challenges in biocomputing is to enable the efficient use of a wide variety of rapidly evolving computational methods to simulate, analyze and understand the complex interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molecular surfaces and the derivation of phenomenological p...

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258-338), while examples of previously known domains with...

Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary stru...

Proteins are the main perpetrators of most cellular tasks. However, they seldom act alone and most biological processes are carried out by macromolecular assemblies and regulated through a complex network of protein-protein interactions. Thus, modern molecular and cell biology no longer focus on single macromolecules but now look into complexes, pathways or even entire organisms. The many genom...

Summary: 3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed ...

Computer-aided design is one of the critical components of modern drug discovery. Drug development is routinely streamlined using computational approaches to improve hit identification and lead selection, to enhance bioavailability, and to reduce toxicity. In the last decade, a mounting body of genomic knowledge has been accumulated due to advancements in genome-sequencing technologies, present...

prolactin is mainly secreted by the anterior pituitary and is able to stimulate mammary gland development and lactation in mammalians. although prolactins share a common ancestral gene encoding, they show species specific characteristics and their efficiency may be different in various mammals. the importance of protein structures of all sequences of this hormone have been studied by various bi...

UNLABELLED We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of...

Sandor Vajda,* Ilya A. Vakser, Michael J.E. Sternberg, and Joël Janin Biomedical Engineering, Boston University, Boston, Massachusetts Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina Structural Bioinformatics, Department of Biological Sciences, Imperial College, London, United Kingdom Laboratoire d’Enzymologie et Biochimie Structur...