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11.
Is there an approach for optimizing the specific binding of antibodies to target cells?
Ario De Marco, invited lecture at foreign university

Keywords: Nanobodies, avidity, modeling, off-target accumulation
Published in RUNG: 31.01.2017; Views: 4371; Downloads: 0
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12.
From Trajectory Modeling to Social Habits and Behaviors Analysis
Donatella Gubiani, Marco Pavan, 2016, independent scientific component part or a chapter in a monograph

Abstract: In recent years, the widespread of mobile devices has made easier and popular the activities of recording locations visited by users and of inferring their trajectories. The availability of such large amount of spatio-temporal data opens new challenges to automatically extract information and get valuable knowledge. The many aspects of this issue have aroused the interest of researchers in several areas, such as information retrieval, data mining, context-aware computing, security and privacy issues, urban planning, and transport management. Recently, there has been a strong interest in understanding how people move during their common daily activities in order to get information about their behaviors and habits. In this paper we describe considerable recent research works related to the analysis of mobile spatio-temporal data, focusing on the study of social habits and behaviors. We provide a general perspective on studies on human mobility by depicting and comparing methods and algorithms, highlighting some critical issues related to information extraction from spatio-temporal data, and future research directions.
Keywords: Trajectory modeling, Social habits and behaviors, Spatio-temporal data, Data mining
Published in RUNG: 18.11.2016; Views: 4767; Downloads: 0
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13.
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Miguel Soler, Ario De Marco, Sara Fortuna, 2016, original scientific article

Abstract: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Keywords: nanobodies, molecular dynamics, modeling, antibody solubility
Published in RUNG: 11.10.2016; Views: 4772; Downloads: 244
.pdf Full text (1,95 MB)

14.
Computational design of customised nanobodies for biotechnological applications
Miguel Soler, Ario De Marco, Sara Fortuna, 2016, unpublished conference contribution

Abstract: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Keywords: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Published in RUNG: 26.04.2016; Views: 4780; Downloads: 0
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