List of works - Francisco Melo

A composite score for predicting errors in protein structure models

scientific article

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

scientific article

A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs

scientific article published on 6 March 2010

A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity

scientific article

A tool to assist the study of specific features at protein binding sites

scientific article

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.

scientific article

Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

scientific article

Adaptive evolution of the insulin gene in caviomorph rodents

scientific article

All-atom knowledge-based potential for RNA structure prediction and assessment

scientific article

Andrographolide activates the canonical Wnt signalling pathway by a mechanism that implicates the non-ATP competitive inhibition of GSK-3β: autoregulation of GSK-3β in vivo

scientific article published in March 2015

Assessing protein structures with a non-local atomic interaction energy.

scientific article

Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile

scientific article published on 2 August 2011

Characterization of small RNAs in X. tropicalis gastrulae

scientific article

Characterization of small RNAs in Xenopus tropicalis gastrulae

scientific article

Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium

scientific article published in June 2007

Comparative protein structure modeling of genes and genomes

scientific article (publication date: 2000)

Comparison of different melting temperature calculation methods for short DNA sequences

scientific article published on 22 October 2004

Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function

scientific article published on 13 March 2012

Decorin is specifically solubilized by heparin from the extracellular matrix of rat skeletal muscles

scientific article published on 01 March 1993

Effective knowledge-based potentials

scientific article

Effects of tetrahydrohyperforin in mouse hippocampal slices: neuroprotection, long-term potentiation and TRPC channels

scientific article published in January 2014

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

scientific article

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs.

scientific article

Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes.

scientific article published on 25 September 2017

Expression of transposable elements in neural tissues during Xenopus development

scientific article

Fold assessment for comparative protein structure modeling.

scientific article

Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages

scientific article

Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

scientific article

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming

scientific article

Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions

article

Molecular and population analyses of a recombination event in the catabolic plasmid pJP4.

scientific article published on October 2006

Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models.

scientific article

Novel knowledge-based mean force potential at atomic level

Novel α-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides

scientific article

Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 grown under carbon-sufficient, nitrogen-limited enological conditions

scientific article published on 21 September 2012

PDIviz: analysis and visualization of protein-DNA binding interfaces

scientific article

Quantitative analysis of wine yeast gene expression profiles under winemaking conditions

article

SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation

scientific article published on 10 July 2007

Scoring Functions for Protein Structure Prediction

article published in 2008

StAR: a simple tool for the statistical comparison of ROC curves

scientific article

Statistical potentials for fold assessment ⬇️

scientific article published on February 1, 2002

Structure-based characterization of multiprotein complexes

scientific article published on 19 June 2014

The Protein-DNA Interface database

scientific article

The internal region leucine-rich repeat 6 of decorin interacts with low density lipoprotein receptor-related protein-1, modulates transforming growth factor (TGF)-β-dependent signaling, and inhibits TGF-β-dependent fibrotic response in skeletal musc

scientific article

Towards the bridging of molecular genetics data across Xenopus species

scientific article

Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments

scientific article

WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures

scientific article

dnaMATE: a consensus melting temperature prediction server for short DNA sequences

scientific article

List of works by Francisco Melo

A composite score for predicting errors in protein structure models

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs

A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity

A tool to assist the study of specific features at protein binding sites

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.

Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

Adaptive evolution of the insulin gene in caviomorph rodents

All-atom knowledge-based potential for RNA structure prediction and assessment

Andrographolide activates the canonical Wnt signalling pathway by a mechanism that implicates the non-ATP competitive inhibition of GSK-3β: autoregulation of GSK-3β in vivo

Assessing protein structures with a non-local atomic interaction energy.

Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile

Characterization of small RNAs in X. tropicalis gastrulae

Characterization of small RNAs in Xenopus tropicalis gastrulae

Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium

Comparative protein structure modeling of genes and genomes

Comparison of different melting temperature calculation methods for short DNA sequences

Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function

Decorin is specifically solubilized by heparin from the extracellular matrix of rat skeletal muscles

Effective knowledge-based potentials

Effects of tetrahydrohyperforin in mouse hippocampal slices: neuroprotection, long-term potentiation and TRPC channels

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs.

Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes.

Expression of transposable elements in neural tissues during Xenopus development

Fold assessment for comparative protein structure modeling.

Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages

Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming

Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions

Molecular and population analyses of a recombination event in the catabolic plasmid pJP4.

Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models.

Novel knowledge-based mean force potential at atomic level

Novel α-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides

Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 grown under carbon-sufficient, nitrogen-limited enological conditions

PDIviz: analysis and visualization of protein-DNA binding interfaces

Quantitative analysis of wine yeast gene expression profiles under winemaking conditions

SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation

Scoring Functions for Protein Structure Prediction

StAR: a simple tool for the statistical comparison of ROC curves

Statistical potentials for fold assessment ⬇️

Structure-based characterization of multiprotein complexes

The Protein-DNA Interface database

The internal region leucine-rich repeat 6 of decorin interacts with low density lipoprotein receptor-related protein-1, modulates transforming growth factor (TGF)-β-dependent signaling, and inhibits TGF-β-dependent fibrotic response in skeletal musc

Towards the bridging of molecular genetics data across Xenopus species

Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments

WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures

dnaMATE: a consensus melting temperature prediction server for short DNA sequences