A5071471999- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- HIV/AIDS drug development and treatment
- Advanced biosensing and bioanalysis techniques
- HIV Research and Treatment
- Chemical Synthesis and Analysis
- Monoclonal and Polyclonal Antibodies Research
- vaccines and immunoinformatics approaches
- Glycosylation and Glycoproteins Research
- Ion Transport and Channel Regulation
- Genomics and Phylogenetic Studies
- Membrane-based Ion Separation Techniques
- 2D Materials and Applications
- Blood Coagulation and Thrombosis Mechanisms
- Blood properties and coagulation
- Genetics, Bioinformatics, and Biomedical Research
- Surface Chemistry and Catalysis
- Machine Learning in Materials Science
- Asymmetric Hydrogenation and Catalysis
- Ion channel regulation and function
Parthenope University of Naples
2015-2024
King Abdullah University of Science and Technology
2013-2020
Naples Anesthesia & Physician Associates
2016-2018
University of Salerno
2009-2014
University of Naples Federico II
2000-2013
European Bioinformatics Institute
2009-2010
Wellcome Trust
2009-2010
Sapienza University of Rome
2007
Accademia Nazionale dei Lincei
2006
Institute of Molecular Biology and Pathology
2005
Developing more efficient catalysts remains one of the primary targets organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present Web application for analyzing catalytic pocket metal complexes using topographic steric maps as general unbiased descriptor that is suitable every class catalysts. show broad applicability our approach, first compared map series transition presenting popular...
Herein we present COCOMAPS, a novel tool for analyzing, visualizing and comparing the interface in protein-protein protein-nucleic acids complexes. COCOMAPS combines traditional analyses 3D visualization of with effectiveness intermolecular contact maps.COCOMAPS is accessible as public web at http://www.molnac.unisa.it/BioTools/cocomapsromina.oliva@uniparthenope.it; lcavallo@unisa.it.
Abstract We present the results for CAPRI Round 54, 5th joint CASP‐CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21 941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified...
We present the results for CAPRI Round 30, first joint CASP-CAPRI experiment, which brought together experts from protein structure prediction and protein-protein docking communities. The comprised 25 targets amongst those submitted CASP11 experiment of 2014. included mostly homodimers, a few homotetramers, two heterodimers, chains that could readily be modeled using templates Protein Data Bank. On average 24 groups 7 CASP predictions each target, 12 per target participated in scoring...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The has case fatality ratio of 3-6% and, recently, multi-country outbreak the occurred. currently available vaccines that have provided immunization against monkeypox are classified as live attenuated vaccinia virus-based vaccines, which pose challenges safety efficacy in chronic infections. In this study, we used an immunoinformatics-aided design multi-epitope vaccine (MEV) candidate by targeting virus...
Candida dubliniensis is an opportunistic pathogen associated with oral and invasive fungal infections in immune-compromised individuals. Furthermore, the emergence of C. antifungal drug resistance could exacerbate its treatment. Hence, this study a multi-epitope vaccine candidate has been designed using immunoinformatics approach by targeting secreted aspartyl proteinases (SAP) proteins. In silico tools have utilized to predict epitopes determine their allergic potential, antigenic toxicity,...
Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain diversity their structures and functions. A significant fraction experimental available date present modified nucleobases, with half them being involved in H-bonding interactions other bases, i.e. 'modified base pairs'. Herein we a systematic investigation pairs, context structures. To this end, first compiled an atlas experimentally observed for which recorded occurrences...
The specific folding pattern and function of RNA molecules lies in various weak interactions, addition to the strong base-base pairing stacking. One these relatively characterized by stacking O4' atom a ribose on top heterocycle ring nucleobase, has been known occur but largely ignored description structures. We identified 2015 ribose-base interactions high-resolution set non-redundant crystal They are widespread structured located structural motifs other than regular stems. Over 50% them...
Canine circovirus (CanineCV) is a deadly pathogen affecting both domestic and wild carnivores including dogs. No vaccine against CanineCV available commercially or under clinical trials. In the present study, we have designed promising multiepitope (MEV) construct targeting multiple strains of CanineCV. A total 545 MHCII binding CD4+T cell epitope peptides were predicted from capsid replicase protein each strain Five conserved among three selected. The final was constructed using antigenic,...
Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis quantum mechanics approach to calculate accurate energies of most frequent tertiary base pairing interactions. Our indicates that six out nine classical held place mainly by H-bonds between bases. In remaining three cases other effects have be considered. interaction range from −8 −38 kcal/mol yeast tRNAPhe estimated contribute roughly 25% overall energy. Six analyzed...
The G15–C48 Levitt base pair, located at a crucial position in the core of canonical tRNAs, assumes reverse Watson–Crick (RWC) geometry. By means bioinformatics analysis and quantum mechanics calculations we show here that such geometry is moderately more stable than an alternative bifurcated trans geometry, involving guanine face cytosine keto group, which have also found known RNA structures. However demonstrate RWC can take advantage additional stabilizing effects as metal binding or...
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one most extreme aquatic environments on Earth, Deep Lake Antarctica (-18 °C to +11.5 and 21-28%, w/v salt content). Hence, H. has been proposed as a model for biotechnology astrobiology investigate potential life beyond Earth. To understand mechanisms that allow proteins adapt both salinity cold, we structurally (including X-ray crystallography molecular dynamics simulations)...
Mitochondrial ribosomal protein large 24 (MRPL24) is 1 of the 82 components mitochondrial ribosomes, playing an essential role in translation process. We report here on a baby girl with cerebellar atrophy, choreoathetosis limbs and face, intellectual disability combined defect complexes I IV muscle biopsy, caused by homozygous missense mutation identified MRPL24. The variant predicts Leu91Pro substitution at evolutionarily conserved site. Using human mutant cells zebrafish model, we...
Abstract Reliably scoring and ranking candidate models of protein complexes assigning their oligomeric state from the structure crystal lattice represent outstanding challenges. A community‐wide effort was launched to tackle these The latest resources on interfaces were exploited derive a benchmark dataset consisting 1677 homodimer structures, including balanced mix physiological non‐physiological complexes. in selected bury similar or larger interface area than counterparts, making it more...
Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used methods TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, studies regulation eukaryotes frequently require numerous PWM models TFBSs due to a large number TFs involved. To overcome these problems we developed DRAF, novel method for that requires only 14 232 human TFs, while at same time significantly...
The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt pair in the context of tRNAs, is a structurally and functionally important that contributes to tertiary interactions joining distant domains functional RNA molecules participates metabolite binding riboswitches. We previously indicated isolated W:W trans rather unstable geometry, dicationic metal Guanine or posttranscriptional modification can increase its stability. Herein, we extend our survey report on other...
The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates SARS-CoV-2 entry into host cells. “fusion core” heptad repeat 1 (HR1) on plays a crucial role in virus infectivity, as it part key membrane fusion architecture. While was becoming global threat, scientists have been accumulating data at an impressive pace, both terms genomic sequences and three-dimensional structures. On 15 February 2021, from GISAID...
This study presents a comprehensive theoretical exploration of the fluorescent non-natural emissive nucleobases- mth A, G, C, and U derived from methylthieno[3,4- d ]pyrimidine heterocycle.
Aquaporins are homotetrameric channel proteins, which allow the diffusion of water and small solutes across biological membranes. According to their transport function, aquaporins can be divided into “orthodox aquaporins”, flux molecules only, “aquaglyceroporins”, facilitate glycerol other in addition water. The contribution individual residues pore selectivity orthodox aquaglyceroporins is not yet fully understood. To gain insights aquaporin selectivity, we focused on sequence variation...