Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands

REVIEW : Recent advances in developing web-servers for predicting protein attributes

“…Although the recently developed state-of-the-art NMR technique is a very powerful in determining the 3D structures of membrane proteins [87,[92][93][94]148], it is time-consuming and costly. In order to timely obtain the protein 3D structures for rational drug design, the approach of structural bioinformatics has been often adopted (see, e.g., [84,[149][150][151][152][153]). Unfortunately, such an approach fails to work in most GPCR-related cases because very few GPCRs have sufficiently high sequence similarity with existing structure-known proteins, an indispensable condition for developing a reasonable starting structure via structural bioinformatics [2,3].…”

“…For further information about protein folding, refer to a recent review [214] and the references cited therein. Again, although it is quite successful to predict the 3D structure of a protein according to the homology modeling approach [2,215] as reflected by a series of homology-modeled proteins for drug development [84,147,[149][150][151]153,[216][217][218][219][220][221][222][223][224][225][226], a hurdle exists when the query protein does not have any structure-known homologous protein in the existing databases [3].…”

Determination of inter- and intra-subtype/species varia-tions in polymerase acidic protein from influenza A virus using amino-acid pair predictability

“…Currently, the manufactured vaccines are designed to target the influenza A virus according to their subtypes, for example, the focus in recent year would be the H5N1 subtype of influenza A virus [7,8,9,10,11,12,13,14], and anti-flu drugs are designed to target neuraminidases and M2 protein [15,16]. It would be understandable that proteins should be different from one subtype to another.…”

Pemanfaatan bioinformatika dalam bidang pertanian dan kesehatan (The utilization of bioinformatics in the field of agriculture and health)

“…Penggunaan piranti-piranti lunak daring tersebut banyak diarahkan untuk pengembangan obat dengue, avian influenza, dan kanker serviks (Wei et al, 2006;Lim et al, 2013;Bakri et al, 2014). Secara lebih detail, beberapa aspek penting dalam desain obat in silico meliputi: (1) metode komputasional pada polifarmakologi, (2) prediksi parameter farmakokinetik, (3) teknologi CADD pada desain obat secara in silico, (4) prediksi potensial aksi, (5) aplikasi OMICs di biologi sel punca, (6) komputasi basis data lncRNAs berbasis internet dibahas di dalam kajian ilmiah ini.…”