Proceedings of the 3rd International Conference on Computation for Science and Technology

+ Advanced search
35 articles

Exploration of Residue Binding Energy of Potential Ankyrin for Dengue Virus II from MD Simulations

Wei Lim Chong, Sharifuddin M. Zain, Noorsaadah Abd. Rahman, Rozana Othman, Shatrah Binti Othman, Piyarat Nimmanpipug, Chatchai Tayapiwatana, Vannajan Sanghiran Lee
Computational approach was employed to evaluate the binding activity of potential ankyrin and domain III of the envelope protein of dengue virus II. Ankyrin serves as an alternative to antibody due to several advantages. Both the ankyrin and domain III were docked using Z-dock protocol in Discovery Studio...

Virtual Screening of 2-hydroxy-1,4-naphthoquinone Derivatives as Antimitotic Agent using Molegro Virtual Docker on Polo Like Kinase 1

Susi Kusumaningrum, Soleh Kosela, Wahono Sumaryono, Emil Budianto, Alfan Danny Arbianto
Naphthoquinone is one of secondary metabolites that are widespread in nature and found in large amounts [1]. Naphthoquinones are clinically important antitumor drugs containing a quinone moiety, such as anthracyclines, mitoxantrones and saintopin, show excellent anticancer activity [2]. In the previouse...

Reducing Computational Complexity of Network Analysis using Graph Compression Method for Brand Awareness Effort

Andry Alamsyah, Yahya Peranginangin, Budi Rahardjo, Intan Muchtadi-Alamsyah, Kuspriyanto
Online social media provides platform for social interactions. This platform produce large-scale data generated mostly from online conversations. Network analysis can help us to mine knowledge and pattern from the relationship between actors inside the network. This approach has been crucial in supporting...

Molecular Docking and Molecular Dynamics Simulation of the Interaction of Cationic Imidazolium Porphyrin-Anthraquinone and Hsp90

Muhammad Arba, Rahmana Emran Kartasasmita, Daryono H. Tjahjono
Hsp90 is involved in the progressiveness of cancer cell through the activation of oncogenic client proteins, including Her2/ErbB2, Akt, Raf-1, and hTERT. Thus, targeting Hsp90 is considered as one of promising strategy in anti-cancer drug development. In the search of new potential Hsp90 inhibitors,...

Complexes Formation of Porphyrin Derivatives with Lead: Preliminary Computational Study of Porphyrin as Analytical Reagent

Rimadani Pratiwi, Slamet I. Surantaatmadja, Daryono H. Tjahjono
Interaction of three cationic porphyrins: meso-tetrakis (N-methylpyridinium-4-yl) porphyrin (H2TMPyP), meso-tetrakis (1,3-dimethylimidazolium-2-yl)porphyrin (H2TDMImP), and meso-tetrakis(1,2-dimethylpyrazolium-4-yl) porphyrin (H2TDMPzP) with lead have been performanced computationally using DFT method....

Prediction of Hazard Identification and Characterization of Several Compounds used as Food Additives Applying In Silico Methods

Iltizam Nasrullah, Rahmana Emran Kartasasmita, Sophi Damayanti
In frame of risk analysis, hazard identification and characterization are parts of risk assessment that should be performed to assure the safety aspect of a substance that will be used as food additive. According to WHO guidance, the two steps can be performed experimentally, based on epidemiological...

Binding Models of Polyphenols to Cytochrome P450 2C9: A Molecular Docking Study

Siripat Chaichit, Darunee Hongwiset, Supat Jiranusornkul
Polyphenols are widely presented in plants and dietary supplements. The beneficial effects of these compounds have been demonstrated, including the prevention of cardiovascular diseases, osteoporosis, neurogenerative diseases and diabetes. From previous studies, polyphenols showed the inhibitory effect...

Investigation of H(2H) - Pt(111) Interaction System: using Density Functional Methods

Can Dogan Vurdu, Muhammet Serdar Cavus, Fatma Kandemirli
In this study, interaction system of hydrogen (two hydrogen) with Pt(111) surface has been investigated theoretically by using density functional theory DFT method. With respect to the definitions of interactions of H-Pt(111) and 2H-Pt(111), the potential energy curves PECs belonging to these interactions...

The Quantum Chemical Calculations of Some Thiazole Derivatives

Murat Saracoglu, Fatma Kandemirli, Mohammed Amin, Can Dogan Vurdu, Muhammet Serdar Cavus, Gokhan Say ner
An examination of quantum chemical and corrosion inhibition studies for some thiazole derivatives, namely 2-amino-4-(p-tolyl)thiazole (APT), 2-methoxy-1,3-thiazole (MTT) and thiazole-4-carboxaldehyde (TCA) had been tested as corrosion safe inhibitors for mild steel (CRS) in 0.5 M H2SO4 solutions at 25...

Modeling of Dirac Electron Tunneling Current in Bipolar Transistor Based on Armchair Graphene Nanoribbon Using a Transfer Matrix Method

Endi Suhendi, Rifky Syariati, Fatimah Noor, Neny Kurniasih, Khairurrijal
The Dirac electron tunneling current in an n-p-n bipolar transistor based on armchair graphene nanoribbon (AGNR) has been modeled. The electron wavefunction was derived by employing the relativistic Dirac equation. The transmittance was derived by using the transfer matrix method (TMM). The Landauer...

Artifacts Removal of EEG Signals using Adaptive Principal Component Analysis

Arjon Turnip, Dwi Esti Kusumandari
Analysis of EEG activity usually raises the problem of differentiating between genuine EEG activity which is introduced through a variety of external influence. These artifacts may affect the outcome of the EEG recording. In this paper, wavelet denoising and band pass filter for preprocessing and an...

In Silico Study of Andrographolide as Protease Inhibitors for Antimalarial Drug Discovery

Sandra Megantara, Jutti Levita, Slamet I. Surantaatmadja
Malaria parasite encodes several homologues of aspartic proteases such as plasmepsin I, II and IV which are responsible for degradation of host erythrocyte hemoglobin inside the vacuole of parasite food. Hence plasmepsins are novel targets for antimalarial drug discovery. Previous study concluded that...

Study on CCR5 Receptor Antagonists as an Anti-Prostate Cancer: Inhibition Activity, QSAR and Molecular Docking

Nursamsiar, Lina Nurfadhila, Iman S. Pratama, Aiyi Asnawi, Slamet I. Surantaatmadja
Chemokine receptor CCR5, a G protein-coupled receptor (GPCR), has been shown as a viable target in drug discovery due to its involvement in HIV entry and cancer. In HIV pathogenesis, CCR5 acts as an essential co-receptor for HIV invasion into host cells; whereas in cancer, it provides a pro-inflammatory...

Interactions of Porphyrin-Acridine Hybrids to DNA Duplexes and Quadruplex: In Silico Study

Hubbi Nashrullah Muhammad, Sophi Damayanti, Daryono H. Tjahjono
The binding modes of cationic porphyrin hybrids to DNA has been studied in a previous study. In the present research, cationic porphyrin-acridine hybrids bearing meso-substituted pyridine, imidazole, and pyrazole rings were investigated for their interaction with DNA. AutoDock Vina was used to dock 11...

Absorption, Distribution and Toxicity Prediction of Curculigoside A and its Derivatives

Nursamsiar, Slamet I. Surantaatmadja, Daryono H. Tjahjono
Curculigoside A is a major bioactive phenolic glycoside of the medicinal plant of Curculigo orchioides. The present study was intended to obtain detail information of the pharmacokinetic properties including oral absorption, distribution, metabolism and toxicity of curculigoside A and its derivatives...

Acetylation of Asiatic Acid and Its Hepatotoxicity Prediction

Ida Musfiroh, Ita Puspitasari, Ahmad Muhtadi, Rahmana E. Kartasasmita, Slamet I. Surantaatmadja
Asiatic acid (AA) is one of the triterpenoids isolated from pegagan (Centella asiatica (L.) Urb.), which has the antiinflammatory activity. The present studies were aimed to synthesize triacetyl asiatic acid (2,3,23-triacetooxy-12-ene asiatic acid) and to predict its hepatotoxicity properties. Acetylation...

Computational Design of Dengue Type-2 NS2B/NS3 Protease Inhibitor: 2D/3D QSAR of Quinoline and Its Molecular Docking

Maywan Hariono, Ezatul E. Kamarulzaman, Habibah Wahab
The reemergence of dengue outbreak demands an effective and efficient treatment especially for antiviral agent since neither vaccine nor drug is available to overcome this disease. This study designed the new model for Dengue Type-2 (DENV2) NS2B/NS3 protease inhibitor from quinoline scaffold by combining...

Molecular Dynamics Simulation on Designed Antibodies of HIV-1 Capsid Protein (p24)

Hana Atiqah Abdul Karim, Chatchai Tayapiwatana, Piyarat Nimmanpipug, Sharifuddin M. Zain, Noorsaadah Abdul Rahman, Vannajan Sanghiran Lee
Computational approaches have been used by the molecular biologists all around the world as a vital tool in developing and improving the functional and binding properties of proteins, particularly antibody-antigen (Ab-Ag) complexes. Based on a previous work, it has been identified that several residues...

Computational Alanine Scanning Mutagenesis: Characterizing the hotspots of ILK-Ankyrin Repeat and PINCH1 Complex

Vertika Gautam, Nadia Hanim Sabri, Wei Lim Chong, Sharifuddin M. Zain, Noorsaadah Abd. Rahman, Vannajan Sanghiran Lee, Anand Gaurav
From the last two decades, computational alanine scanning mutagenesis (cASM) have been successively applied to a variety of protein complexes to study the energetics and structural characteristics of hot spot residues at protein interface. The cASM combines a continuum approach to model solvent interactions...

Molecular Docking Studies of Flavonoids of Noni Fruit (Morinda citrifolia L.) to Peroxisome Proliferator-Activated Receptor-Gamma (PPAR )

Fikry Awaluddin, Andrianopsyah Mas Jaya Putra, Supandi Supandi
Diabetes is a chronic disease that occurs either when the pancreas does not produce enough insulin or when the body cannot effectively use the produced insulin. Morinda citrifolia has been widely used as herbal medicine to prevent and to treat diabetes as well as health supplements. It contains flavonoids...

Model Identification of Continuous Fermentation under Noisy Measurements

Rudy Agustriyanto
The dynamic model concept plays a central role in automatic control. Understanding the dynamic behavior of chemical and biological processes depends first on understanding the steady state behavior of these processes, then the dynamic characteristics of the process (e.g., the time constant, gain and...

Acceleration of norm-conserving Pseudopotential Plane-Wave-Based DFT Calculation on GPU using CUDA

F. Fathurahman, Enngar Alfianto, H. K. Dipojono, M. A. Martoprawiro
In present study, acceleration of density functional theory calculation using norm-conserving pseudopotential and plane wave (NCPP-PW) basis set has been performed. It did not use or parallelize commonly program packages (such as ABINIT, VASP, PWSCF, etc.) but propose prototypical program to carry out...

Pyrazolylporphyrin Derivatives as New Potential Ligand for Melanoma Cancer Radiopharmaceutical Kit: In Silico Study

Fransiska Kurniawan, Rahmana Emran Kartasasmita, Daryono H. Tjahjono
Melanoma is the most lethal skin cancer, and it is related to Fibroblast Growth Factor 2 (FGF2) which is important for survival and proliferation of melanocytes. Diagnosis and therapy of melanoma cancer can be performed applying radiopharmaceutical with appropriate ligand. The aim of this research was...

Toxicity Prediction of meso-5,15-di[3,4-bis(carboxymethylenoxy)phenyl] porphyrin and meso-5,15-di[3,4-bis(carboxymethylenoxy)phenyl],10,20-diphenyl porphyrin

Fauzan Zein Muttaqin, Slamet I. Surantaatmadja, Abdul Mutalib, Daryono H. Tjahjono
Porphyrin and its derivatives are widely investigated for cancer therapy because of their high selectivity to cancer cells. By labeling gamma and beta emitting-radionuclides to a porphyrin which selectively binds to the cancer tissue will produce a safe and potential radiopharmaceutical. The present...

QSAR Study of Quinazoline Derivatives as Inhibitor of Epidermal Growth Factor Receptor-Tyrosine Kinase (EGFR-TK)

La Ode Aman, Widisusanti Abdulkadir, Julitha Geybie Rembet, Daryono H. Tjahjono
Nowadays a lot of new active substances as anticancer cervix agents have been developed. One of the protein targets in discovery of anticancer cervix drugs is Epidermal Growth Factor Receptor-Tyrosine Kinase (EGFR-TK). In this present research the Quantitative Structure and Activity Relationship (QSAR)...

Cembranoid Diterpenes as Antitumor: Molecular Docking Study to Several Protein Receptor Targets

Muhammad S. Zubair, Syariful Anam, Khalid O. Al-Footy, Ahmed Abdel-Lateef, Walied M. Alarif
A molecular docking analysis has been carried out on several cytotoxic cembaranoid type diterpenes that have been isolated from soft coral Sarcophyton glaucum i.e sarcophytolol, sarcophytolide B, sarcophytolide C, sarcophine, deoxosarcophine, and cembrene C. All the compounds were investigated using...

Numerical Analysis on the Stability Behavior of a Dynamical System on the Deposit and Loan of a Bank

Novriana Sumarti, H. Fansuri
A dynamical system is one of sophisticated techniques using mathematical equations that can determine the observed state for all future times based on the current state. It will also show small changes in the state of the system create either small or big changes in the future depending on the model....

Implementation of Finite Field Arithmetic Operations for Polynomial and Normal Basis Representations

Mirza Maulana, Wenny Franciska Senjaya, Budi Rahardjo, Intan Muchtadi-Alamsyah, Marisa W. Paryasto
Elliptic Curve Cryptography is generally are implemented over prime fields or binary fields. Arithmetic in binary elds can be classified according to the basis representation being used. Two of the most common basis used in binary elds are polynomial basis and normal basis. The optimal normal basis is...

Construction of Tetha-Cyclic Codes over an Algebra of Order 4

Intan Muchtadi-Alamsyah, Aleams Barra, Ahmad Muchlis, Djoko Supriyanto, Irwansyah
In this paper, we show that tetha-cyclic codes over algebra A1 = F2+vF2 can be constructed from binary cyclic codes using a bijection map from A1 to F2 X F2. We also give a decoding algorithm for tetha-cyclic codes which are constructed using well-known BCH codes over binary field.

Surface Interaction between Ethylene, Hydroxide Ion, and Titanium Dioxide Anatase (001): A First Principle Density Functional Theory Study

Paulus Himawan, Mohammad Kemal Agusta, Hermawan Kresno Dipojono, Ganes Shukri, Nugraha
This study covers surface interaction between ethylene, hydroxide ion, and Ti5C adsorption site of titanium dioxide anatase (001). The result of the relaxation suggests that stability was reached on Ti5C site with the adsorption energy of -0.57 eV, while the changes in the bond length and angle between...

Structural Study of Chalcogenide Material Ge-Te-Ga using ab Initio Molecular Dynamics

Lilin Lalita, H. K. Dipojono, M. A. Martoprawiro
Due to its capability of quick amorphous-crystalline phase transition, chalcogenide material Ge-Te-Ga is a potential candidate of a phase change material. For the amorphous phase, the dominant bonding is between Ga and Te. The first peak of Ga-Te bonds is at about 2.7 Å. In the liquid phase, on the other...

In Silico Study of The Component of Eleutherine americana MERR. on Human Estrogen Reseptor Alpha as Potential Anti-Breast Cancer

Tasia Amelia, Dina Pratiwi, Romsiah, Daryono H. Tjahjono
Eleutherine americana (Indonesian: “bawang dayak”) has been used traditionally to treat breast cancer by Borneo people. Its compounds contains eleutherine, eleutherinone, eleutherol, isoeleutherine, eleutherinol, dihydroeleutherinol, hongconin, and 6,8-dihydroxy-3,4-dimethoxy-1-methyl-anthraquinone-2-carboxylic...

Discovering Inhibitors of Tyrosinase Enzyme from Zingiberaceae for Depigmentation Agents

Karina Muthia, Fride Rindu Alami, Nyi Mekar Saptarini, Jutti Levita
Tyrosinase enzyme, which has two copper ions in its catalytic site, involved in skin pigmentation by catalyzing three oxidation reactions on melanogenesis, that are conversion of L-tirosine to L-DOPA, L-DOPA to dopaquinone, and 5,6-dihydroxyindole to 5,6-indolequinone. An inhibition of melanogenesis...

Docking of Dengue NS2B-NS3 Protease with Murraya koenigii

Kai Sing Yong, Sy Bing Choi, Habibah Wahab
Dengue disease has been reported for more than 100 million cases every year distressing tropical and subtropical countries. Dengue virus carries a positive single strand RNA, belongs to Flaviviridae family consist of four serotypes give rise to undifferentiated fever, dengue fever (DF), dengue hemorrhagic...

Computer-aided Structure-based Design of 3,3'-Diallyl-[1,1'-biphenyl]- 4,4'- diol Analogs of Eugenol as Potential Ligands for Estrogen Receptor Alpha

Enade Perdana Istyastono, Yulia Anita, Andini Sundowo
The SBVS protocols to identify ligands for estrogen receptor alpha (ER ) were retrospectively validated and could serve as a virtual tool to screen potential ER ligands. Subsequently, prospective virtual screen campaigns on eugenol analogs and their dimers were performed and have discovered 3,3'-diallyl-[1,1'-biphenyl]-4,4'-diol...