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Author

Alessandro Pedretti

Other affiliations: University of Lausanne
Bio: Alessandro Pedretti is an academic researcher from University of Milan. The author has contributed to research in topics: Docking (molecular) & Virtual screening. The author has an hindex of 26, co-authored 113 publications receiving 3038 citations. Previous affiliations of Alessandro Pedretti include University of Lausanne.


Papers
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Journal ArticleDOI
TL;DR: The expandability and flexibility features of the VEGA program are presented, for the development of custom applications, using it as a multipurpose graphical environment.
Abstract: In this paper we present the expandability and flexibility features of the VEGA program (downloadable free of charge at http://www.ddl.unimi.it), for the development of custom applications, using it as a multipurpose graphical environment. VEGA can be customized using both plug-in architecture and script programming. The first is useful to add new features and functions, using homemade routines, written with the VEGA Plug-in Development Kit (SDK). With the second approach it is possible to design scripts in VEGA, using the REBOL language, in order to (1) add new functions or customize existing ones; (2) automate common procedures; and (3) allow network communications, by creating a bridge between VEGA and other applications (or other PCs) through the TCP/IP protocol.

663 citations

Journal ArticleDOI
TL;DR: The program VEGA is proposed, that was developed to create a bridge between the most popular molecular software packages, and some features are implemented some features to analyze, display and manage the three dimensional structure of the molecules.
Abstract: We here propose the program VEGA, that was developed to create a bridge between the most popular molecular software packages. In this tool some features are implemented some features to analyze, display and manage the three dimensional (3D) structure of the molecules. The most important features are (1) file format conversion (with assignment of the atom types and atomic charges), (2) surface calculation and (3) trajectory analysis. The executable and the source code can be free downloaded from [URL: see text].

420 citations

Journal ArticleDOI
TL;DR: As it is demonstrated, molecules are not 'frozen statues' but 'dancing ballerinas', and several of their computable physicochemical properties are conformation-dependent and lead to the concept of property spaces, which appears as a promising descriptor to encode some of the information contained in molecular property spaces.

220 citations

Journal ArticleDOI
TL;DR: An overview of the compared quantitative importance of biotransformation reactions in the metabolism of drugs and other xenobiotics is offered, based on a meta-analysis of current research interests, and the relative significance the enzyme (super)families or categories catalysing these reactions are assessed.

174 citations

Journal ArticleDOI
TL;DR: This review considers the main systems directly involved in type 2 diabetes mellitus or involved in diabetes comorbidities and considers the multi-target approaches involved in the treatment of this type of diabetes.
Abstract: Diabetes Mellitus (DM) is a multi-factorial chronic health condition that affects a large part of population and according to the World Health Organization (WHO) the number of adults living with diabetes is expected to increase. Since type 2 diabetes mellitus (T2DM) is suffered by the majority of diabetic patients (around 90–95%) and often the mono-target therapy fails in managing blood glucose levels and the other comorbidities, this review focuses on the potential drugs acting on multi-targets involved in the treatment of this type of diabetes. In particular, the review considers the main systems directly involved in T2DM or involved in diabetes comorbidities. Agonists acting on incretin, glucagon systems, as well as on peroxisome proliferation activated receptors are considered. Inhibitors which target either aldose reductase and tyrosine phosphatase 1B or sodium glucose transporters 1 and 2 are taken into account. Moreover, with a view at the multi-target approaches for T2DM some phytocomplexes are also discussed.

158 citations


Cited by
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Journal ArticleDOI
TL;DR: Anautomatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity are presented.
Abstract: In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

4,124 citations

Journal ArticleDOI
TL;DR: Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades and theory behind the most important methods and recent successful applications are discussed.
Abstract: Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.

1,362 citations

Journal ArticleDOI
TL;DR: In this paper, the authors provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive quantitative structure-activity relationship models.
Abstract: Quantitative structure–activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR stu...

1,314 citations

Journal ArticleDOI
01 Mar 1994-Nature
TL;DR: It is clear that the above can lead to confusion when scientists of different countries are trying to communicate with each other, so an internationally recognized system of naming organisms is created.
Abstract: It is clear that the above can lead to confusion when scientists of different countries are trying to communicate with each other. Another example is the burrowing rodent called a gopher found throughout the western United States. In the southeastern United States the term gopher refers to a burrowing turtle very similar to the desert tortoise found in the American southwest. One final example; two North American mammals known as the elk and the caribou are known in Europe as the reindeer and the elk. We never sing “Rudolph the Red-nosed elk”! Confused? This was the reason for creating an internationally recognized system of naming organisms. To avoid confusion, living organisms are assigned a scientific name based on Latin or Latinized words. The English sparrow is Passer domesticus or Passer domesticus (italics or underlining these two names is the official written representation of a scientific name). Using a uniform naming system allows scientists from all over the world to recognize exactly which life form a scientist is referring to. The naming process is called the binomial system of nomenclature. Passer is comparable to a surname and is called the genus, while domesticus is the specific or species name (like your given name) of the English sparrow. Now scientists can give all sparrow-like birds the genus Passer but the species name will vary. All similar genera (plural for genus) can be grouped into another, “higher” category (see below). Study the following for a more through understanding of taxonomy. Taxonomy Analogy Kingdom: Animalia Country

1,305 citations

Journal ArticleDOI
TL;DR: The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions, which supports a wide variety of force fields.
Abstract: The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field The package runs on Linux, macOS, and Windows systems In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations

800 citations