Publications

β-Roll-targeting peptide and Ectoine synergy: A novel strategy to impair dengue NS1 function

Nur Indra, Asep Iin, Aditama, Reza, Ihsanawati, Hertadi, Rukman

DOI: 10.1016/j.ijbiomac.2025.145856

Enhanced production of polyhydroxybutyrate in recombinant Escherichia coli for sustainable material

Rizki, Wa Ode Sri, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.1016/j.nxmate.2025.101050

Rhamnolipid-Modified PHB-Ectoine Nanoparticles for Multifunctional Skin Protection Against UVB, Irritation, and Bacteria

Tyara Simbara, Alma; Faridatul Habibah, Fera; Hertadi, Rukman

DOI: 10.1021/acsomega.4c10583

Development of inulin nanocarrier for effective oral delivery of insulin: synthesize, optimization, characterization, and biophysical study

Rasjava, Achmad Ramadhanna’il, Kurniawati, Desy, Rizki, Wa Ode Sri, Kurniati, Neng Fisheri, Hertadi, Rukman

DOI: 10.1080/09205063.2024.2436297

Study on the development of nanoparticles based on levan for oral insulin delivery

Kurniawati, Desy, Kurniati, Neng Fisheri, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.1088/1748-605X/adb22d

Engineered acetylated inulin nanoparticles for enhanced oral insulin delivery: sustained release, structural stability, and in vivo efficacy

Rasjava, Achmad Ramadhanna'il, Kurniati, Neng Fisheri, Hertadi, Rukman

DOI: https://doi.org/10.1039/D5RA03627E

Designing a Novel Multiepitope Vaccine from the Human Papilloma Virus E1 and E2 Proteins for Indonesia with Immunoinformatics and Molecular Dynamics Approaches

Rizarullah; Aditama, Reza; Arifin Giri-Rachman, Ernawati; Hertadi, Rukman

DOI: 10.1021/acsomega.4c00425

In Silico Study, Design, and Expression of an Intranasal Dual Chimeric Vaccine for Indonesian-Based Norovirus GII-2 and Hepatitis B

Giri-Rachman, Ernawati Arifin, Tan, Marselina Irasonia, Intan, Novia Syari, Fajar, Putri Ayu, Wojciechowska, Gladys Emmanuella Putri, Hertadi, Rukman, Retnoningrum, Debbie Soefie

DOI: 10.4308/hjb.31.5.1007-1018

Physicochemical characterization of biodegradable polymer polyhydroxybutyrate from halophilic bacterium local strain Halomonas elongata

Rizki, W.O.S., Komariah, S., Andini, D.G.T., Simbara, A.T., Ratnaningsih, E., Hertadi, R.

DOI: 10.22034/gjesm.2024.03.12

Green synthesis of copper ions nanoparticles functionalized with rhamnolipid as potential antibacterial agent for pathogenic bacteria

Habibah, Fera Faridatul, Sri Rizki, Wa Ode, Ivansyah, Atthar Luqman, Astuti, Dea Indriani, Hertadi, Rukman

DOI: 10.1016/j.heliyon.2024.e24242

Leveraging protein language model embeddings and logistic regression for efficient and accurate in-silico acidophilic proteins classification

Susanty, Meredita, Mursalim, Muhammad Khaerul Naim, Purwarianti, Ayu, LE Rajab, Tati, Hertadi, Rukman, Mursalim, Muhammad Khaerul Naim

DOI: 10.1016/j.compbiolchem.2024.108163

Classifying alkaliphilic proteins using embeddings from protein language model

Susanty, Meredita, Naim Mursalim, Muhammad Khaerul, Hertadi, Rukman, Purwarianti, Ayu, Rajab, Tati LE.

DOI: 10.1016/j.compbiomed.2024.108385

Fabrication of physically crosslink Levan-lsbl-bk1/PVA electrospun nanofiber

Abdillah, Bagus Furqan, Nasir, Muhamad, Mozef, Tjandrawati, Hertadi, Rukman

DOI: 10.1016/j.eurpolymj.2023.112237

EmbedCaps-DBP: Predicting DNA-Binding Proteins Using Protein Sequence Embedding and Capsule Network

Naim, Muhammad Khaerul, Mengko, Tati Rajab, Hertadi, Rukman, Purwarianti, Ayu, Susanty, Meredita

DOI: 10.1109/ACCESS.2023.3328960

Development of Chimeric Hepatitis B (HBV) – Norovirus (NoV) P particle as candidate vaccine against Hepatitis B and norovirus infection

Giri-Rachman, Ernawati Arifin, Irasonia Tan, Marselina, Ramesh, Ashwin, Fajar, Putri Ayu, Nurul Ilmi, Annisa, Retnoningrum, Debbie Sofie, Hertadi, Rukman, Irawan, Apriliani, Wojciechowska, Gladys Emmanuella Putri, Yuan, Lijuan

DOI: 10.1016/j.jvacx.2023.100354

BiCaps-DBP: Predicting DNA-binding proteins from protein sequences using Bi-LSTM and a 1D-capsule network

Mursalim, Muhammad K.N., Mengko, Tati L.E.R., Hertadi, Rukman, Purwarianti, Ayu, Susanty, Meredita

DOI: 10.1016/j.compbiomed.2023.107241

Graphene quantum dots functionalised with rhamnolipid produced from bioconversion of palm kernel oil by Pseudomonas stutzeri BK-AB12MT as a photocatalyst

Habibah, Fera Faridatul, Ivansyah, Atthar Luqman, Ivan, Samuel, Hertadi, Rukman

DOI: 10.1039/d2ra05967c

Production of poly-(R)-3-hydroxybutyrate from halophilic bacterium Salinivibrio sp. utilizing palm oil mill effluent as a carbon source

Rizki, Wa Ode Sri, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.1016/j.bcab.2022.102558

Synthesis of pyridinium-based ionic liquids and their application to improve Candida rugosa lipase stability in a methanol-water solvent system

Hendra Cipta, Oktavianus, Alni, Anita, Hertadi, Rukman

DOI: 10.55730/1300-0527.3539

In Silico Study on Predicting Effects of H243L Mutation in Bacillus subtilis Levansucrase towards Sucrose Binding Affinity

Sudijanto, Jason Andrew, Hertadi, Rukman

DOI: 10.4028/p-43hm23

A Review of Extremophile Protein Classification Using Machine Learning

Susanty, Meredita, Rajab, Tati Latifah Erawati, Hertadi, Rukman

DOI: 10.1109/ICWT55831.2022.9935440

Low Complexity Classification of Thermophilic Protein using One Hot Encoding as Protein Representation

Susanty, Meredita, Hertadi, Rukman, Purwarianti, Ayu, Rajab, Tati Latifah Erawati

DOI: 10.14569/IJACSA.2022.0131212

Potential Application of Rhamnolipid-Silica Nanoparticle Complex for Enhanced Oil Recovery Studied with Molecular Dynamics Simulations

Fitri, Ika Keumala, Ivansyah, Atthar Luqman, Hertadi, Rukman

DOI: 10.4028/p-c099ku

Cloning, Expression, and In Silico Analysis of Class IV Poly-(R)-3hydroxybutyrate Genes from New Strain of Bacillus thuringiensis TH-01

Sabiqoh, Zuhdina, Hertadi, Rukman, Ratnaningsih, Enny

DOI: 10.4308/hjb.29.3.310-319

Recombinant expression and biochemical characterization of levansucrase from halophilic bacteria bacillus licheniformis BK1 and BK2

Permatasari, Nur Umriani, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.4028/www.scientific.net/KEM.874.96

Isolation and characterization of poly-(R)-3-hydroxybutyrate produced by bacillus thuringiensis th-01

Rizki, Wa Ode Sri, Sabiqoh, Zuhdina, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.4028/www.scientific.net/KEM.874.81

Box-wilson design for optimization of in vitro levan production and levan application as antioxidant and antibacterial agents

Hertadi, Rukman, Permatasari, Nur Umriani, Ratnaningsih, Enny

DOI: 10.29252/ibj.25.3.202

A Review of Protein Structure Prediction using Deep Learning

Susanty, Meredita, Rajab, Tati Erawati, Hertadi, Rukman

DOI: 10.1051/bioconf/20214104003

Molecular docking simulation of interaction between insulin and silica nanoparticle

Hertadi, R., Ivansyah, A.L.

DOI: 10.1088/1742-6596/1869/1/012062

Molecular dynamics study of candida rugosa lipase in water, methanol, and pyridinium based ionic liquids

Cipta, Oktavianus Hendra, Alni, Anita, Hertadi, Rukman

DOI: 10.4028/www.scientific.net/KEM.874.88

Short communication: Ability of ectoine to stabilize lipase against elevated temperatures and methanol concentrations

Parwata, I. Putu, Wahyuningrum, Deana, Suhandono, Sony, Hertadi, Rukman

DOI: 10.22146/ijc.54931

Prediction of protein tertiary structure using pre-Trained self-supervised learning based on transformer

Kurniawan, Alif, Jatmiko, Wisnu, Hertadi, Rukman, Habibie, Novian

DOI: 10.1109/IWBIS50925.2020.9255624

Process optimization of palm oil mill effluent-based biosurfactant of Halomonas meridiana BK-AB4 originated from bledug kuwu mud volcano in central java for microbial enhanced oil recovery

Sari, Cut Nanda, Hertadi, Rukman, Harahap, Andre Fahriz Perdana, Ramadhan, Muhammad Yusuf Arya, Gozan, Misri

DOI: 10.3390/PR8060716

Isolation and characterization of a surfactant-stable protease from halophilic bacteria chromohalobacter japonicus bk-ab18

Achmad, Dwi Isyana, Ihsanawati, Hertadi, Rukman

DOI: 10.55230/mabjournal.v49i2.1520

Levan produced by the halophilic bacterium Bacillus licheniformis BK1 as a nanoparticle for protein immobilization

Oktavia, Ira, Fithriah, Aidah Nur, Permatasari, Nur Umriani, Ratnaningsih, Enny, Hertadi, Rukman

DOI: 10.22146/ijc.41064

Enhancement of antioxidant activity of levan through the formation of nanoparticle systems with metal ions

Hertadi, Rukman, Amari, Muzayana Mahbuba Saleha, Ratnaningsih, Enny

DOI: 10.1016/j.heliyon.2020.e04111

Effect of calcium ions to the activity and stability of extracellular lipase produced by moderate halophilic bacteria Halomonas meridiana BK-AB4

Nanda, Galo Ayu Megga, Hertadi, Rukman

DOI: 10.55230/mabjournal.v49i2.1519

The Effects of Microwave-Assisted Pretreatment and Cofermentation on Bioethanol Production from Elephant Grass

Kolo, Sefrinus Maria Dolfi, Wahyuningrum, Deana, Hertadi, Rukman

DOI: 10.1155/2020/6562730

Biosynthesis and characterization of bioplastic polyhydroxybutyrate from halophilic bacterium Halomonas elongata BK-AB8

Rachmawati, Rachmawati, Falahuddin, Wendi, Hertadi, Rukman

DOI: 10.4028/www.scientific.net/KEM.811.28

Heterologous ectoine production in Escherichia coli: Optimization using response surface methodology

Parwata, I Putu, Wahyuningrum, Deana, Suhandono, Sony, Hertadi, Rukman

DOI: 10.1155/2019/5475361

Estimating factors determining emulsification capability of surfactant-like peptide with coarse-grained molecular dynamics simulation

Wijaya, Tegar, Hertadi, Rukman

DOI: 10.22146/ijc.34547

Processing of ozonized biodiesel waste to produce biosurfactant using Pseudomonas aeruginosa for enhanced oil recovery

Sari, Cut Nanda, Fatimah, Izzah Nur, Hertadi, Rukman, Gozan, Misri

DOI: 10.1063/1.5095032

Production and characterization of rhamnolipids from bioconversion of palm oil mill effluent by the halophilic bacterium Pseudomonas stutzeri BK-AB12

Fazli, Rahmad Rizki, Hertadi, Rukman

DOI: 10.1002/ep.13007

Factors Affecting the Production of Biosurfactants and their Applications in Enhanced Oil Recovery (EOR). A Review

Sari, C.N., Hertadi, R., Gozan, M., Roslan, A.M.

DOI: 10.1088/1755-1315/353/1/012048

Bioconversion of glycerol to biosurfactant by halophilic bacteria Halomonas elongata BK-AG18

Alvionita, Mieke, Hertadi, Rukman

DOI: 10.22146/ijc.26737

In Silico Study of Phospholipids as An Oral Insulin Delivery System

Fuadah, Nanik Rahmawati, Hertadi, Rukman

DOI: 10.1088/1742-6596/1090/1/012053

Production of ectoine by Halomonas elongata BK-AG25 using osmotic shock technique

Putu Parwata, I., Wahyuningrum, Deana, Suhandono, Sony, Hertadi, Rukman

DOI: 10.1088/1755-1315/209/1/012017

Optimization of rhamnolipid production from bioconversion of palm oil mill effluent (POME) waste by Pseudomonas stutzeri BK-AB12 using response surface methodology

Fazli, Rahmad Rizki, Hertadi, Rukman

DOI: 10.1088/1755-1315/209/1/012024

The use of response surface method in optimization of levan production by heterologous expressed levansucrase from halophilic bacteria bacillus licheniformis BK2

Permatasari, N.U., Ratnaningsih, E., Hertadi, R.

DOI: 10.1088/1755-1315/209/1/012015

Molecular modeling on porphyrin derivatives as β5 subunit inhibitor of 20S proteasome

Arba, Muhammad, Nur-Hidayat, Andry, Ruslin, Yusuf, Muhammad, Sumarlin, Hertadi, Rukman, Wahyudi, Setyanto Tri, Surantaadmaja, Slamet Ibrahim, Tjahjono, Daryono H.

DOI: 10.1016/j.compbiolchem.2018.03.002

Bioconversion of palm oil into biosurfactant by halomonas meridiana BK-AB4 for the application of corrosion inhibitor

Sari, Ira Prima, Basyiruddin, Muhammad Imam, Hertadi, Rukman

DOI: 10.22146/ijc.27040

Determination of activities of human carbonic anhydrase ii inhibitors from curcumin analogs

Aditama, Reza, Eryanti, Yum, Mujahidin, Didin, Syah, Yana Maolana, Hertadi, Rukman

DOI: 10.4314/tjpr.v16i4.14

Polyhydroxybutyrate (PHB) production by Halomonas elongata BK AG 18 indigenous from salty mud crater at central Java Indonesia

Hertadi, Rukman, Kurnia, Kurnia, Falahudin, Wendy, Puspasari, Made

Exploring levan-producing bacteria chromohalobacter japonicus bk-Ab 18 for biobeneficiation of bauxite through the investigation of its levansucrase properties

Hertadi, Rukman, Nasir, Daris Qodarisman, Mufti, Nandang

Determination of the reactivity of the anti-cancer nitrogen mustard-mechlorethamine: A cyclic voltammetric investigation

Setiyanto, Henry, Saraswaty, Vienna, Hertadi, Rukman, Buchari, Buchari

A new strategy of glucose supply in a microbial fermentation model

Kasbawati, Gunawan, A.Y., Sidarto, K.A., Hertadi, R.

DOI: 10.1063/1.4930637

Metabolic regulation and maximal reaction optimization in the central metabolism of a yeast cell

Kasbawati, Gunawan, A.Y., Hertadi, R., Sidarto, K.A.

DOI: 10.1063/1.4914436

Cloning and sequence analysis of lipase gene of halophilic bacteria isolated from mud crater of Bledug Kuwu, Central Java, Indonesia

Asyari, Mukhammad, Aditiawati, Pingkan, Akhmaloka, Hertadi, Rukman

DOI: 10.13005/bbra/1856

Isolation and identification of halostable lipase producing bacteria from the Bledug Kuwu mud crater located at Purwodadi-Grobogan, Central Java, Indonesia

Asy'ari, Mukhammad, Parwata, I. Putu, Aditiawati, Pingkan, Akhmaloka, Hertadi, Rukman

Simple and easy method to synthesize chicken eggshell based Hydroxyapatite

Tri Wahyudi, Setyanto, Utami Dewi, Setia, Anggraeni, Ajeng, Dahlan, Kiagus, Akhmaloka, Ali Zulfikar, Muhammad, Hertadi, Rukman

DOI: 10.4028/www.scientific.net/AMR.896.276

Effects of time delay on the dynamics of a kinetic model of a microbial fermentation process

Kasbawati, Gunawan, A.Y., Hertadi, R., Sidarto, K.A.

DOI: 10.1017/S1446181114000194

Organic solvent-stable lipase from moderate halophilic bacteria Pseudomonas stutzeri isolated from the mud crater of Bleduk Kuwu, Central Java, Indonesia

Parwata, I. Putu, Asyari, Mukhamad, Hertadi, Rukman

Thermostable alkaline lipase isolated from thermus aquaticus

Febriani, Ihsanawat, Hertadi, Rukman, Madayanti, Fida, Akhmaloka

Removal of humic acid from peat water using untreated powdered eggshell as a low cost adsorbent

Zulfikar, M.A., Novita, E., Hertadi, R., Djajanti, S.D.

DOI: 10.1007/s13762-013-0204-5

The role of electrostatic interactions on Klentaq1 insight for domain separation

Nurbaiti, Santi, Martoprawiro, Muhamad A., Akhmaloka, Hertadi, Rukman

DOI: 10.4137/BBI.S9390

Cyclic voltammetric study of chlorambucil in the presence of 4-chloro butyronitrile in aqueous solution

Setiyanto, Henry, Saraswaty, Vienna, Hertadi, Rukman, Noviandri, Indra, Buchari, Buchari

Chemical reactivity of chlorambucil in organic solvents: Influence of 4-chloro butyronitrile nucleophile to voltammogram profiles

Setiyanto, Henry, Saraswaty, Vienna, Hertadi, Rukman, Noviandri, Indra, Buchari, Buchari

DOI: 10.1016/s1452-3981(23)18169-7

Individual domain stability of Klenow-like DNA Pol I ITB-1 based on molecular dynamic simulation

Helwati, Hira, Nurbaiti, Santi, Hertadi, Rukman, Warganegara, Fida Madayanti, Akhmaloka

Isolation and purification of novel thermostable alkaline lipase from local thermophilic microorganism

Febriani, Hertadi, Rukman, Kahar, Prihardi, Akhmaloka, Madayanti, Fida

Domain motions of Klenow-like DNA polymerase I ITB-1 in the absence of substrate

Nurbaiti, Santi, Nagao, Hidemi, Saito, Hiroaki, Hertadi, Rukman, Martoprawiro, Muhamad A, Akhmaloka

Interface domain interactions on early stage unfolding of DNA polymerase I Klenow fragment

Nurbaiti, Santi, Hertadi, Rukman, Martoprawiro, Muhamad A., Akhmaloka

Construction, expression and purification of DNA Pol I ITB1 and its deletion mutants

Helwati, Hira, Hertadi, Rukman, Madayanti, Fida, Akhmaloka

Dynamics of protein extraction and extension by force spectroscopy and molecular dynamics simulation

Ikai, Atsushi, Afrin, Rehana, Hertadi, Rukman, Ohta, Satoko

DOI: 10.1063/1.1764146

Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy

Hertadi, Rukman, Gruswitz, Franz, Silver, Lin, Koide, Akiko, Koide, Shohei, Arakawa, Hideo, Ikai, Atsushi

DOI: 10.1016/j.jmb.2003.09.010

Unfolding mechanics of holo- and apocalmodulin studied by the atomic force microscope

Hertadi, Rukman, Ikai, Atsushi

DOI: 10.1110/ps.3600102