1. Compression of triangulated solids’ surfaces by Decimating Reconstructable TrianglesBlaž Repnik, Borut Žalik, Krista Rizman Žalik, 2025, izvirni znanstveni članek Opis: This paper introduces a new programming solution for reducing the size of files needed to store 3D geometric solids, whose surfaces are interpolated by watertight irregular triangle meshes. Unlike other approaches, the software does not introduce any special storage data format, but, instead, utilises popular CAD formats such as STL, OBJ, or PLY. This increases the software’s interoperability significantly. The software comprises an encoder and a decoder. The encoder estimates which facets may be removed in such a way that they can later be reconstructed unambiguously by the decoder. The decoder also ensures that the reconstructed triangles are oriented correctly. The encoder and the decoder are straightforward to understand and to implement. They are asymmetric, making any potential programming error easier to identify and correct. Ključne besede: data compression, geometric modelling, computer-aided design, boundary representation, topology, watertightness Objavljeno v DKUM: 30.05.2025; Ogledov: 0; Prenosov: 2
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2. Commercial SARS-CoV-2 targeted, protease inhibitor focused and protein–protein interaction inhibitor focused molecular libraries for virtual screening and drug designSebastjan Kralj, Marko Jukič, Urban Bren, 2022, pregledni znanstveni članek Opis: Since December 2019, the new SARS-CoV-2-related COVID-19 disease has caused a global
pandemic and shut down the public life worldwide. Several proteins have emerged as potential
therapeutic targets for drug development, and we sought out to review the commercially available
and marketed SARS-CoV-2-targeted libraries ready for high-throughput virtual screening (HTVS).
We evaluated the SARS-CoV-2-targeted, protease-inhibitor-focused and protein–protein-interactioninhibitor-focused libraries to gain a better understanding of how these libraries were designed. The
most common were ligand- and structure-based approaches, along with various filtering steps, using
molecular descriptors. Often, these methods were combined to obtain the final library. We recognized
the abundance of targeted libraries offered and complimented by the inclusion of analytical data;
however, serious concerns had to be raised. Namely, vendors lack the information on the library
design and the references to the primary literature. Few references to active compounds were also
provided when using the ligand-based design and usually only protein classes or a general panel
of targets were listed, along with a general reference to the methods, such as molecular docking for
the structure-based design. No receptor data, docking protocols or even references to the applied
molecular docking software (or other HTVS software), and no pharmacophore or filter design
details were given. No detailed functional group or chemical space analyses were reported, and no
specific orientation of the libraries toward the design of covalent or noncovalent inhibitors could
be observed. All libraries contained pan-assay interference compounds (PAINS), rapid elimination
of swill compounds (REOS) and aggregators, as well as focused on the drug-like model, with the
majority of compounds possessing their molecular mass around 500 g/mol. These facts do not bode
well for the use of the reviewed libraries in drug design and lend themselves to commercial drug
companies to focus on and improve. Ključne besede: targeted libraries, focused libraries, computer-aided drug design, virtual screening, in silico drug design, high-throughput virtual screening Objavljeno v DKUM: 09.04.2025; Ogledov: 0; Prenosov: 7
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3. Identification of furin protease small-molecule inhibitor with a 1,3-thiazol-2-ylaminosulfonyl scaffoldAnja Kolarič, Vid Ravnik, Sara Štumpf Horvat, Marko Jukič, Urban Bren, 2025, izvirni znanstveni članek Ključne besede: computer-assisted drug design, CADD, computer-assisted drug design, furin inhibitors, protease inhibitors, antivirals, protease inhibitors, furin assay, antiviral drug design Objavljeno v DKUM: 20.03.2025; Ogledov: 0; Prenosov: 3
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4. Molecular Filters in Medicinal ChemistrySebastjan Kralj, Marko Jukič, Urban Bren, 2023, pregledni znanstveni članek Ključne besede: medicinal chemistry, filtering chemical libraries, chemical space, HTVS, virtual screening, computer aided drug-design, in silico drug design, bioinformatics, chemoinformatic, compound library Objavljeno v DKUM: 20.05.2024; Ogledov: 168; Prenosov: 26
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5. Neuropilin (NRPs) related pathological conditions and their modulatorsMatic Broz, Anja Kolarič, Marko Jukič, Urban Bren, 2022, pregledni znanstveni članek Opis: Neuropilin 1 (NRP1) represents one of the two homologous neuropilins (NRP, splice variants of neuropilin 2 are the other) found in all vertebrates. It forms a transmembrane glycoprotein distributed in many human body tissues as a (co)receptor for a variety of different ligands. In addition to its physiological role, it is also associated with various pathological conditions. Recently, NRP1 has been discovered as a coreceptor for the SARS-CoV-2 viral entry, along with ACE2, and has thus become one of the COVID-19 research foci. However, in addition to COVID-19, the current review also summarises its other pathological roles and its involvement in clinical diseases like cancer and neuropathic pain. We also discuss the diversity of native NRP ligands and perform a joint analysis. Last but not least, we review the therapeutic roles of NRP1 and introduce a series of NRP1 modulators, which are typical peptidomimetics or other small molecule antagonists, to provide the medicinal chemistry community with a state-of-the-art overview of neuropilin modulator design and NRP1 druggability assessment. Ključne besede: neuropilins, computer-aided drug design, in silico drug design, receptor modulator design, peptidomimetics, small-molecule antagonists, cancer, COVID-19, neuropathic pain Objavljeno v DKUM: 22.08.2023; Ogledov: 379; Prenosov: 375
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6. GAJA : 3-D CAD methodology for developing a parametric system for the automatic (re)modeling of compound washer dies' cutting-componentsDavid Potočnik, Bojan Dolšak, Miran Ulbin, 2013, izvirni znanstveni članek Opis: Although the designing of cutting-dies is a complex and experience-based process, it is poorly supported by conventional 3D CAD software. Thus, the majority of design activities, including the (re)modeling of those cutting die-components that are directly responsible for performing shaping operations on a sheet-metal stamping part, traditionally still need to be carried-out repetitively, separately, and manually by the designer. In order to eliminate some of these drawbacks and upgrade the capabilities of conventional 3D CAD software, this paper proposes a new methodology for the development of a parametric system capable of automatically performing a (re)modeling process of compound washer diesć cutting-components. The presented methodology integrates CATIA V5 built-in modules, including Part Design, Assembly Design and Knowledge Advisor, publication mechanism, and compound cutting die-design knowledge. The system developed by this methodology represents an 'intelligent' assembly template composed of two modules 'GAJA1' and 'GAJA2', respectively. 'GAJA1' is responsible for the direct input of the die-design problem regarding the shape, dimensions and material of the stamping part, its extraction in the form of geometric features, and the transferring of relevant design parameters and features to the module 'GAJA2'. 'GAJA2' interprets the current values for the input parameters and automatically performs the modeling process of cutting die-components, using die-design knowledge and the company's internal design and manufacturing standards. Experimental results show that the use of this system significantly shortens the modeling-time for cutting the die-components, improves the modeling-quality, and enables the training of inexperienced designers. Ključne besede: parametrično modeliranje, rezalna orodja, računalniško podprti sistemi, inteligentno računalniško podprto konstruiranje, parametric modeling, cutting dies, computer-aided systems, knowledge-based design Objavljeno v DKUM: 10.07.2015; Ogledov: 3207; Prenosov: 55
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7. Uvajanje računalniško podprte proizvodnjeUroš Trupej, 2013, diplomsko delo Opis: V svoji diplomski nalogi sem se osredotočil na uvajanje računalniško podprte proizvodnje in kakšne prednosti prinaša. Računalniško podprta proizvodnja združuje moderno računalniško tehnologijo z naprednimi obdelovalnimi stroji in povezavo z informacijskim sistemom, kjer je človek še vedno vodilo napredka. Na teoretičnem primeru sem prikazal kakšne spremembe mora neko podjetje opravit in kakšne pogoje mora zadostiti, da lahko uvede računalniško podprto proizvodnjo. Ključne besede: RIP - Računalniško integrirana proizvodnja, CIM - Computer integrated manufacturing, CAD - Computer Aided Design.CAM - Computer Aided Manufacturing, CAE - Computer Aided Engeneering, CAQ - Computer Aided Quality Assurance, CAPP - Computer Aideded Process Planning, CABS - Computer Aideded Business Sysytem, CAST - Computer Aideded Storagee and Transport, CNC - Computer Numerical Control, POS - Prilagodljivi obdelovalni stroji Objavljeno v DKUM: 16.10.2013; Ogledov: 2154; Prenosov: 232
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8. CD-ROM to accompany The data model resource bookLen SilverstonKljučne besede: information systems, MIS, data structure, data, warehousing, data warehousing, models, data base, CD-ROM, computer diskette, enterprise, products, ordering sets, business function, human resource management, human resources, sampling, design, application, modelling, electronic commerce Objavljeno v DKUM: 01.06.2012; Ogledov: 4116; Prenosov: 176
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10. Layered additive manufacturing in clinical medicineIgor Drstvenšek, Nataša Ihan Hren, Tadej Strojnik, Vojko Pogačar, Tjaša Zupančič Hartner, Andreja Sinkovič, 2008, izvirni znanstveni članek Opis: The use of contemporary technologies of Computer Assisted Design (CAD), combined with latest rapid prototyping, tooling and manufacturing, with traditional CT scanning techniques and high medical skills are used as instruments for better diagnostic visualization, simulation of procedures and treatment of patients with craniofacial deformities. They also improve the overall performances of medical and nursing staff thus influencing the quality of medical service. Patients with congenital defects, orthognathic deformities, deformities after malignancy treatment or after craniofacial traumatic injuries of different severities are of particular interests due to both aesthetic and functional alterations. The paper presents two clinical cases - a patient with scull bone defect after brain hemorrhage and brain edema as well as a patient with hemifacial microsomia treated by surgery followed by implantation of titanium angular implant prepared by means of computer tomography scans, Computer Aided Design and Rapid Manufacturing technologies. Ključne besede: rapid prototyping, computer assisted design, maxilla, scull, reconstructive surgery Objavljeno v DKUM: 31.05.2012; Ogledov: 2356; Prenosov: 149
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