ORCID Profile
0000-0001-6979-8469
Current Organisation
Federal University of Itajuba
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Publisher: Oxford University Press (OUP)
Date: 12-05-2020
DOI: 10.1093/BIOINFORMATICS/BTAA480
Abstract: EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters. EasyVS is freely available as an easy-to-use web interface at biosig.unimelb.edu.au/easyvs. douglas.pires@unimelb.edu.au or david.ascher@unimelb.edu.au Supplementary data are available at Bioinformatics online.
Publisher: Wiley
Date: 14-08-2008
DOI: 10.1002/PROT.22187
Abstract: In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse-grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value at about 7.0 A emerges as an important distance parameter. Up to 7.0 A, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when mapping the first layer of neighbors. In proteins, it may produce systematic errors affecting mainly the contact network in beta chains with CA. The almost-Delaunay (AD) approach has been proposed to solve this DT problem. We found that even AD may not be an advantageous solution. As a consequence, in the strict range up to 7.0 A, the CD approach revealed to be a simpler, more complete, and reliable technique than DT or AD. Finally, we have shown that coarse-grained residue representations may introduce bias in the analysis of neighbors in cutoffs up to 6.8 A, with CA favoring alpha proteins and GC favoring beta proteins. This provides an additional argument pointing to the value of 7.0 A as an important lower bound cutoff to be used in contact analysis of proteins.
Publisher: Oxford University Press (OUP)
Date: 24-04-2015
DOI: 10.1093/BIOINFORMATICS/BTV223
Abstract: Summary: PDBest (PDB Enhanced Structures Toolkit) is a user-friendly, freely available platform for acquiring, manipulating and normalizing protein structures in a high-throughput and seamless fashion. With an intuitive graphical interface it allows users with no programming background to download and manipulate their files. The platform also exports protocols, enabling users to easily share PDB searching and filtering criteria, enhancing analysis reproducibility. Availability and implementation: PDBest installation packages are freely available for several platforms at www.pdbest.dcc.ufmg.br Contact: wellisson@dcc.ufmg.br, dpires@dcc.ufmg.br, raquelcm@dcc.ufmg.br Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Oxford University Press (OUP)
Date: 09-12-2201
DOI: 10.1093/BIOINFORMATICS/BTR680
Abstract: Motivation: Protein–protein interfaces contain important information about molecular recognition. The discovery of conserved patterns is essential for understanding how substrates and inhibitors are bound and for predicting molecular binding. When an inhibitor binds to different enzymes (e.g. dissimilar sequences, structures or mechanisms what we call cross-inhibition), identification of invariants is a difficult task for which traditional methods may fail. Results: To clarify how cross-inhibition happens, we model the problem, propose and evaluate a methodology called HydroPaCe to detect conserved patterns. Interfaces are modeled as graphs of atomic apolar interactions and hydrophobic patches are computed and summarized by centroids (HP-centroids), and their conservation is detected. Despite sequence and structure dissimilarity, our method achieves an appropriate level of abstraction to obtain invariant properties in cross-inhibition. We show ex les in which HP-centroids successfully predicted enzymes that could be inhibited by the studied inhibitors according to BRENDA database. Availability: www.dcc.ufmg.br/~raquelcm/hydropace Contact: valdetemg@ufmg.br raquelcm@dcc.ufmg.br santoro@icb.ufmg.br Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Springer Science and Business Media LLC
Date: 12-2011
Publisher: Oxford University Press (OUP)
Date: 08-02-2013
DOI: 10.1093/BIOINFORMATICS/BTT058
Abstract: Motivation: Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design. Results: We propose a novel graph-based–binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor’s techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario. Availability and implementation: Datasets and the source code are available at www.dcc.ufmg.br/∼dpires/acsm. Contact: dpires@dcc.ufmg.br or raquelcm@dcc.ufmg.br Supplementary information: Supplementary data are available at Bioinformatics online.
No related grants have been discovered for Carlos Silveira.