Biomedical subjects

Gonzalo López

Publications and source records attributed to Gonzalo López.

4 recordsLinked to original sources

PubMed2005

Scoring docking models with evolutionary information.

We have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases.

Algorithms↗

PubMed2005

Domain definition and target classification for CASP6.

Assessment of structure predictions in CASP6 was based on single domains isolated from experimentally determined structures, which were categorized into comparative modeling, fold recognition, and new fold targets. Domain definitions were defined upon visual examination of the structures with the aid of automated domain-parsing programs. Domain categorization was determined by comparison of the target structures with those in the Protein Data Bank at the time each target expired and a variety of sequence and structure-based methods to determine potential homologous relationships.

Amino Acid Sequence↗

PubMed2005

Assessment of predictions submitted for the CASP6 comparative modeling category.

Here we present a full overview of the Critical Assessment of Protein Structure Prediction (CASP6) comparative modeling category. Prediction accuracy for the 43 comparative modeling targets was assessed through detailed numerical comparisons between predicted and experimental structures. Assessments using standard measures for model backbone quality and structural alignment accuracy highlighted a small number of groups with stand out predictions and these findings were backed up by statistical comparisons. We were able to carry out evaluations of side-chain contacts predictions and side-chain rotamer accuracy, for which one group turned out to have statistically better predictions. We also assessed the prediction quality of structurally divergent regions and biologically important sites. Interestingly we were able to show that predictors were not predicting these important functional regions with any greater accuracy than the rest of the structure. In addition we investigated the ability of predictors to build models that improve on the structural template and reached some tentative conclusions from comparisons with the previous CASP experiment.

Algorithms↗

PubMed2003

Cross reactivity of three antivenoms against North American snake venoms.

The antivenom in the United States today is in short supply, expensive and may not even be the most effective in neutralizing venoms from snakes in certain geographical locations. The ED(50) is considered to be the best indicator of antivenom efficacy, however, other tests are needed. In this study, three antivenoms (Antivipmyn (Fab(2)H), Crotalidae Polyvalent Immune Fab (Ovine) (FabO) and UCV (FabV) were used to test the effectiveness of neutralization of eight venoms (Agkistrodon piscivorus piscivorus, Bothrops asper, Crotalus adamanteus, C. durissus durissus, C. horridus atricaudatus, C. h. horridus, C. atrox, and C. molossus molossus). Four different assays were used to study the efficacy of the antivenoms: the antihemorrhagic, antigelatinase, antifibrinolytic and antihide powder azure. Fab(2)H antivenom was more effective in neutralizing the enzymatic activities of these eight venoms than FabO and FabV antivenoms.

Animals↗