Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Molecular docking, molecular dynamics, ADME-Tox (4)
- Protein domain annotation, Gene prediction (3)
- GO classification (2)
- HMM models (2)
- Protein domains (2)
-
- Avoidance (1)
- Biokimia dan Teknologi Farmasi: Desain Obat dan Vaksin dengan Pendekatan Biomedis Molekular (1)
- Cavity (1)
- Co-occurrence (1)
- Commercial cylic peptide (1)
- Cyclic peptide (1)
- DNA binding domain (1)
- Dengue (1)
- Envelope protein (1)
- Eukarya (1)
- Functional genome (1)
- Functional genome annota- tion (1)
- Fusion process (1)
- H1N1 (1)
- HMG-box (1)
- HMM (1)
- Molecular Simulation (1)
- SCOP (1)
- Superfamily (1)
- The In Silico Molecular Interaction of Organoboron Compounds as Curative Measure toward Cervical Cancer (1)
- Virology (1)
Articles 1 - 7 of 7
Full-Text Articles in Life Sciences
The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft
The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft
Arli A Parikesit
The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus was devised. The polymerase pac-pb1n enzyme is responsible for the replication of H1N1 virus. Thus, novel inhibitors were developed to ward off the functionality of the enzyme. In this research, cyclic peptides has been chosen to inhibit PAc-PB1n due to its proven stability in reaching the drug target. Thus, computational method for elucidating the molecular interaction between cyclic peptides …
The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft
The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft
Arli A Parikesit
No abstract provided.
Biokimia Dan Teknologi Farmasi: Desain Obat Dan Vaksin Dengan Pendekatan Biomedis Molekular, Usman Sumo Friend Tambunan Usft, Arli A. Parikesit Aap
Biokimia Dan Teknologi Farmasi: Desain Obat Dan Vaksin Dengan Pendekatan Biomedis Molekular, Usman Sumo Friend Tambunan Usft, Arli A. Parikesit Aap
Arli A Parikesit
No abstract provided.
Pitfalls Of Ascertainment Biases In Genome Annotations—Computing Comparable Protein Domain Distributions In Eukarya, Arli A. Parikesit, Lydia Steiner, Peter F. Stadler, Sonja J. Prohaska
Pitfalls Of Ascertainment Biases In Genome Annotations—Computing Comparable Protein Domain Distributions In Eukarya, Arli A. Parikesit, Lydia Steiner, Peter F. Stadler, Sonja J. Prohaska
Arli A Parikesit
Most investigations into the large-scale patterns of protein evolution are based on gene annotations that have been compiled in reference databases. The use of these resources for quantitative comparisons, however, is complicated by sometimes vast differences in coverage. More importantly, however, we also observe substantial ascertainment biases that cannot be removed by simple normalization procedures. A striking example is provided by the correlations between protein domains. We observe that statistics derived from different computational gene annotation procedure show dramatic discrepancies, and even qualitative changes from negative to positive correlation, when compared to statistics obtained from annotation databases.
Screening Of Commercial Cyclic Peptides As Inhibitor Envelope Protein Dengue Virus (Denv) Through Molecular Docking And Molecular Dynamics, Arli A. Parikesit, Kinanty Kinanty, Usman Sumo F. Tambunan
Screening Of Commercial Cyclic Peptides As Inhibitor Envelope Protein Dengue Virus (Denv) Through Molecular Docking And Molecular Dynamics, Arli A. Parikesit, Kinanty Kinanty, Usman Sumo F. Tambunan
Arli A Parikesit
Dengue virus (DENV) has spread throughout the world, especially in tropical climates. Effective treatment of DENV infection is not yet available although several candidate vaccines have been developed. Treatment at this time is only to reduce symptoms and reduce the risk of death. Therefore, antiviral treatment is much needed. Envelope protein is one of the structural proteins of DENV which is known and could be a target of antiviral inhibitors and plays a special role in the fusion process. The aim of this research is to screen the commercial cyclic peptides which are used as inhibitors of envelope protein DENV …
Evolution And Quantitative Comparison Of Genome-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Evolution And Quantitative Comparison Of Genome-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Arli A Parikesit
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show …
Quantitative Comparison Of Genomic-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Quantitative Comparison Of Genomic-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Arli A Parikesit
Investigations into the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains among distantly related genomes. Currently available databases, such as the SUPERFAMILY, are not designed for quantitative comparisons since they are built upon transcript and protein annotations provided by the various different genome annotation projects. Large biases are introduced by the differences in genome annotation protocols, which strongly depend on the availability of transcript information and well-annotated closely related organisms. Here we show that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the …