LightDock: a new multi-scale approach to protein-protein docking.

Motivation: Computational prediction of protein-protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity complexes or transient interactions. A major challenge is how to efficiently sample the structural and energetic landscape of the association at different resolution levels, given that each scoring function is often highly coupled to a specific type of search method. Thus, new methodologies capable of accommodating multi-scale conformational flexibility and scoring are strongly needed. Results: We describe here a new multi-scale protein-protein docking methodology, LightDock, capable of accommodating conformational flexibility and a variety of scoring functions at different resolution levels. Implicit use of normal modes during the search and atomic/coarse-grained combined scoring functions yielded improved predictive results with respect to state-of-the-art rigid-body docking, especially in flexible cases. Availability and implementation: The source code of the software and installation instructions are available for download at https://life.bsc.es/pid/lightdock/. Contact: juanf@bsc.es. Supplementary information: Supplementary data are available at Bioinformatics online.

Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns.

Identifying conserved (similar) three-dimensional patterns among a set of proteins can be helpful for the rational design of polypharmacological drugs. Some available tools allow this identification from a limited perspective, only considering the available information, such as known binding sites or previously annotated structural motifs. Thus, these approaches do not look for similarities among all putative orthosteric and or allosteric bindings sites between protein structures. To overcome this tech-weakness Geomfinder was developed, an algorithm for the estimation of similarities between all pairs of three-dimensional amino acids patterns detected in any two given protein structures, which works without information about their known patterns. Even though Geomfinder is a functional alternative to compare small structural proteins, it is computationally unfeasible for the case of large protein processing and the algorithm needs to improve its performance. This work presents several parallel versions of the Geomfinder to exploit SMPs, distributed memory systems, hybrid version of SMP and distributed memory systems, and GPU based systems. Results show significant improvements in performance as compared to the original version and achieve up to 24.5x speedup when analyzing proteins of average size and up to 95.4x in larger proteins.

Cell-Dock: high-performance protein-protein docking.

SUMMARY: The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality. AVAILABILITY AND IMPLEMENTATION: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock. CONTACT: djimenez@ac.upc.edu or juanf@bsc.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels.

The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. Also, it would be a reasonable first step for the design of novel multitarget compounds. Most of the current computational tools employed for this aim are limited to the comparisons among known binding sites, and do not consider several additional important 3D patterns such as allosteric sites or other conserved motifs. In the present work, we introduce Geomfinder2.0, which is a new and improved version of our previously described algorithm for the deep exploration and discovery of similar and druggable 3D patterns. As compared with the original version, substantial improvements that have been incorporated to our software allow: (i) to compare quaternary structures, (ii) to deal with a list of pairs of structures, (iii) to know how druggable is the zone where similar 3D patterns are detected and (iv) to significantly reduce the execution time. Thus, the new algorithm achieves up to 353x speedup as compared to the previous sequential version, allowing the exploration of a significant number of quaternary structures in a reasonable time. In order to illustrate the potential of the updated Geomfinder version, we show a case of use in which similar 3D patterns were detected in the cardiac ions channels NaV1.5 and TASK-1. These channels are quite different in terms of structure, sequence and function and both have been regarded as important targets for drugs aimed at treating atrial fibrillation. Finally, we describe the in vitro effects of tafluprost (a drug currently used to treat glaucoma, which was identified as a novel putative ligand of NaV1.5 and TASK-1) upon both ion channels' activity and discuss its possible repositioning as a novel antiarrhythmic drug.

Autoimmune pancreatitis diagnosis based on immunoglobulin G4 levels: Case report / Diagnóstico de pancreatitis autoinmune basado en niveles de inmunoglobulina G4: reporte de caso

Abstract Introduction: Autoimmune pancreatitis is a rare form of chronic pancreatitis, with an estimated prevalence of 1 case per 100 000 inhabitants in the general population. It is characterized by the presence of painless obstructive jaundice and imaging findings of a diffusely enlarged pancreas and loss of its lobularity. Depending on its features, it can be classified as subtype 1 or 2, and its diagnosis is reached based on imaging, serological, and histological findings, as well as the patient's response to corticosteroid therapy, which in turn is the indicated treatment for this disease. Case presentation: A 62-year-old man was admitted to the emergency department of a quaternary care hospital in Bogotá D.C. due to generalized jaundice associated with choluria and acholia. Upon admission, the patient was assessed by the general surgery and gastroenterology services and diagnosed with autoimmune pancreatitis based on immunoglobulin G4 levels and imaging and laboratory findings compatible with this disease. He was successfully treated with corticosteroids, obtaining satisfactory clinical outcomes and a complete resolution of symptoms. Conclusions: Autoimmune pancreatitis is a disease that should be suspected in patients with symptoms of painless obstructive jaundice, thus avoiding misdiagnoses and providing timely treatment that allows the resolution of symptoms and proper management of the disease.

Resumen Introducción. La pancreatitis autoinmune es una forma de pancreatitis crónica poco frecuente, con una prevalencia estimada de 1 caso por cada 100 000 habitantes en la población general. Se caracteriza por la presencia de ictericia obstructiva indolora y hallazgos imagenológicos de un páncreas aumentado de tamaño con forma difusa y pérdida de su lobularidad. Se clasifica en subtipo 1 o 2, dependiendo de sus características, y el diagnóstico se realiza de acuerdo con los hallazgos imagenológicos, serológicos, histológicos y la respuesta a la corticoterapia, que a su vez es el tratamiento indicado para esta enfermedad. Presentación del caso. Hombre de 62 años quien ingresó al servicio de urgencias de un hospital de cuarto nivel de atención en Bogotá D.C., Colombia, por cuadro clínico de ictericia generalizada acompañada de coluria y episodios de acolia. Fue valorado por el servicio de cirugía general en conjunto con gastroenterologia y diagnosticado con pancreatitis autoinmune basándose en los niveles de inmunoglobulina G4 y los hallazgos imagenológicos y de laboratorio compatibles con esta enfermedad. El paciente fue tratado de manera exitosa con terapia corticoide, logrando resultados clínicos satisfactorios y resolución de la sintomatologia. Conclusiones. La pancreatitis autoinmune es una enfermedad que debe sospecharse en pacientes con sintomatologia de ictericia obstructiva indolora, evitando de esta forma diagnósticos erróneos y brindando un tratamiento oportuno que permita la resolución de los síntomas y un manejo adecuado de la enfermedad.