4,076 research outputs found
CCharPPI web server: computational characterization of protein–protein interactions from structure
The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework Programme (FP7/2007-
2013) under REA grant agreement PIEF-GA-2012-327899 and grant BIO2013-48213-R from Spanish Ministry of Economy and
Competitiveness.Peer ReviewedPostprint (published version
LightDock: a new multi-scale approach to protein–protein docking
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.
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.B.J-G was supported by a FPI fellowship from the Spanish Ministry of Economy and
Competitiveness. This work was supported by I+D+I Research Project grants BIO2013-48213-R and BIO2016-79930-R from the Spanish Ministry of Economy
and Competitiveness. This work is partially supported by the European Union H2020
program through HiPEAC (GA 687698), by the Spanish Government through Programa
Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and
Technology (TIN2015-65316-P) and the Departament d’Innovació, Universitats i
Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programaciói Entorns d’Execució Paral·lels (2014-SGR-1051).Peer ReviewedPostprint (author's final draft
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
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