Damir Vukičević

Bio: Damir Vukičević is an academic researcher from University of Split. The author has contributed to research in topics: Wiener index & Topological index. The author has an hindex of 26, co-authored 138 publications receiving 2529 citations. Previous affiliations of Damir Vukičević include University of Trieste & University of Kragujevac.

Topological index based on the ratios of geometrical and arithmetical means of end-vertex degrees of edges

Abstract: Research on the topological indices based on end-vertex degrees of edges has been intensively rising recently. Randic index, one of the best-known topological indices in chemical graph theory, is belonging to this class of indices. In this paper, we introduce a novel topological index based on the end-vertex degrees of edges and its basic features are presented here. We named it as geometrical-arithmetic index (GA).

Augmented Zagreb index

Abstract: Inspired by recent work on the atom-bond connectivity (ABC) index we propose here a new topological index, augmented Zagreb index (AZI). The tight upper and lower bounds for chemical trees are obtained. Moreover, it has been shown that among all trees the star has the minimum AZI value. Characterizing trees with maximal augmented Zagreb index remains an open problem for future research.

Bond Additive Modeling 1. Adriatic Indices

Abstract: Some of the most famous molecular descriptors are bond additive, i.e. they are calculated as the sum of edge contributions (Randic-type indices, Balaban-type indices, Wiener index and its modifications, Szeged index...). In this paper, the methods of calculations of bond contributions of these descriptors are analyzed. The general concepts are extracted, and based on these concepts a large class of molecular descriptors is defined. These descriptors are named Adriatic indices. An especially interesting subclass of these descriptors consists of 148 discrete Adriatic indices. They are analyzed on the testing sets provided by the International Academy of Mathematical Chemistry, and it has been shown that they have good predictive properties in many cases. They can be easily encoded in the computer and it may be of interest to incorporate them in the existing software packages for chemical modeling. It is possible that they could improve various QSAR and QSPR studies.

Computational design of highly selective antimicrobial peptides.

Abstract: We have created a structure-selectivity database (AMPad) of frog-derived, helical antimicrobial peptides (AMPs), in which the selectivity was determined as a therapeutic index (TI), and then used the novel concept of sequence moments to study the lengthwise asymmetry of physicochemical peptide properties. We found that the cosine of the angle between two sequence moments obtained with different hydrophobicity scales, defined as the D-descriptor, identifies highly selective peptide antibiotics. We could then use this descriptor to predict TI changes after point mutations in known AMPs, and to aid the prediction of TI for de novo designed AMPs. In combination with an amino acid selectivity index, a motif regularity index and other statistical rules extracted from AMPad, the D-descriptor enabled construction of the AMP-Designer algorithm. A 23 residue, glycine-rich, peptide suggested by the algorithm was synthesized and the activity and selectivity tested. This peptide, adepantin 1, is less than 50% identical to any other AMP, has a potent antibacterial activity against the reference organism, E. coli, and has a significantly greater selectivity (TI > 200) than the best AMP present in the AMPad database (TI = 125).

Kirk-Othmer Encyclopedia of Chemical Technology数据库介绍及实例

Abstract: 介绍了Kirk—Othmer Encyclopedia of Chemical Technology（化工技术百科全书）（第五版）电子图书网络版数据库，并对该数据库使用方法和检索途径作出了说明，且结合实例简单地介绍了该数据库的检索方法。

Designing antimicrobial peptides: form follows function

Abstract: Multidrug-resistant bacteria are a severe threat to public health. Conventional antibiotics are becoming increasingly ineffective as a result of resistance, and it is imperative to find new antibacterial strategies. Natural antimicrobials, known as host defence peptides or antimicrobial peptides, defend host organisms against microbes but most have modest direct antibiotic activity. Enhanced variants have been developed using straightforward design and optimization strategies and are being tested clinically. Here, we describe advanced computer-assisted design strategies that address the difficult problem of relating primary sequence to peptide structure, and are delivering more potent, cost-effective, broad-spectrum peptides as potential next-generation antibiotics.

Variable neighbourhood search: methods and applications

Abstract: Variable neighbourhood search (VNS) is a metaheuristic, or a framework for building heuristics, based upon systematic changes of neighbourhoods both in descent phase, to find a local minimum, and in perturbation phase to emerge from the corresponding valley It was first proposed in 1997 and has since then rapidly developed both in its methods and its applications In the present paper, these two aspects are thoroughly reviewed and an extensive bibliography is provided Moreover, one section is devoted to newcomers It consists of steps for developing a heuristic for any particular problem Those steps are common to the implementation of other metaheuristics

Antimicrobial peptides: key components of the innate immune system

Abstract: Life-threatening infectious diseases are on their way to cause a worldwide crisis, as treating them effectively is becoming increasingly difficult due to the emergence of antibiotic resistant strains. Antimicrobial peptides (AMPs) form an ancient type of innate immunity found universally in all living organisms, providing a principal first-line of defense against the invading pathogens. The unique diverse function and architecture of AMPs has attracted considerable attention by scientists, both in terms of understanding the basic biology of the innate immune system, and as a tool in the design of molecular templates for new anti-infective drugs. AMPs are gene-encoded short (<100 amino acids), amphipathic molecules with hydrophobic and cationic amino acids arranged spatially, which exhibit broad spectrum antimicrobial activity. AMPs have been the subject of natural evolution, as have the microbes, for hundreds of millions of years. Despite this long history of co-evolution, AMPs have not lost their ability to kill or inhibit the microbes totally, nor have the microbes learnt to avoid the lethal punch of AMPs. AMPs therefore have potential to provide an important breakthrough and form the basis for a new class of antibiotics. In this review, we would like to give an overview of cationic antimicrobial peptides, origin, structure, functions, and mode of action of AMPs, which are highly expressed and found in humans, as well as a brief discussion about widely abundant, well characterized AMPs in mammals, in addition to pharmaceutical aspects and the additional functions of AMPs.