Publications

Group highlights

At the end of this page, you can find the full list of publications.

Full List of publications

Cluster Structure and Ordering in the Nucleation and Growth of Binary Molecular Mixtures
Joseph Gregory Z. Cabinta, Earl Adrian D. R. Hans, Roosevelt T. Tabag Jr., Johnrob Y. Bantang, and Ricky B. Nellas
The Journal of Physical Chemistry B

Exploring the effects of N234 and N343 linked glycans to SARS-CoV-2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations
Ronny L. Cheng, James Peter L. Lim, Myrnel A. Fortuna, Donnifer V. Reyes Jr., Earl Adrian D. R. Hans & Ricky B. Nellas
Scientific Reports volume 15, Article number: 7052 (2025)

The Importance of Helical Structures to the Overall Activity and Structural Stability of a Lipase from Pseudomonas aeruginosa PAO1 in n-hexane
Jaidriel Meg Cabanding, Steve Sheng-Fa Yu, Zhi-Han Lin, Myrnal Almoradie-Fortuna, Adam Jo Elatico, and Ricky Nellas
Archives of Biochemistry and Biophysics, p.110226

Interpretable Ensemble Classifiers for Reliable Prediction of Antibacterial Activities of Peptides Against Escherichia Coli and Staphylococcus Aureus
Remmer Salas, Portia Mahal Sabido, and Ricky Nellas.
Available at SSRN 4736138 (2024).

Complementary Pocket and Network-Based Approach to Search for Spike Protein Allosteric Pocket Sites
Ronny Cheng, Jerwin Quirante, Louise Erika Vargas, Abigael Gatchalian, and Ricky Nellas
ACS Omega 2023, 8, 48, 45313–45325

Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study
Jokent Gaza, Ricky Nellas
Journal of Chemical Information and Modeling, 63(15), pp.4654-4663

The role of glycerol–water mixtures in the stability of FKBP12-rapalog-FRB complexes
Joshua Jener Lopez, Jokent Gaza, and Ricky Nellas
Journal of Molecular Graphics and Modelling, 124, p.108556

Specificity of Monoterpene Interactions with Insect Octopamine and Tyramine Receptors: Insights from in Silico Sequence and Structure Comparison
Almira Ocampo, Joseph Gregory Cabinta, Hyvi Valerie Padilla, Eizadora Yu, and Ricky Nellas
ACS omega, 8(4), pp.3861-3871

Identification of Inhibitors of the Schistosoma mansoni VKR2 Kinase Domain
Indran Mathavan, Lawrence J. Liu, Sean W. Robinson, Nelly El-Sakkary, Adam Jo J. Elatico, Darwin Gomez, Ricky Nellas, Raymond J. Owens, William Zuercher, Iva Navratilova, Conor R. Caffrey, and Konstantinos Beis
ACS Medicinal Chemistry Letters, 13(11), pp.1715-1722

Sustainable hues: Exploring the molecular palette of biowaste dyes through LC-MS metabolomics
Ralph John Emerson Molino, Klidel Fae Relin, Ricky Nellas, and Hiyas Junio
Molecules, 26(21), p.664

pH-Dependent Conformations of an Antimicrobial Spider Venom Peptide, Cupiennin 1a, from Unbiased HREMD Simulations
Jokent Gaza, Jarold John Leyson, Gardee Pena, and Ricky Nellas.
ACS omega, 6(37), 24166-24175

Small in size, big on taste: Metabolomics analysis of flavor compounds from Philippine garlic
Ralph John Emerson Molino, Klidel Fae Relin, Ricky Nellas, and Hiyas Junio
Plos one, 16(5), p.e0247289

The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor-retinoid X receptor
James Peter Lim, Mac Kevin Braza, and Ricky Nellas.
Journal of Molecular Graphics and Modelling, 104, p.107829

In Silico Insights on the Allosteric Modulation of the µ-Opioid Receptor and G Protein Complex in the Presence of Agonist Ligand BU72 and Potential Positive Allosteric Modulator BMS-986121
Mac Kevin Braza, Christian Seitz, J. Andrew McCammon, Rommie E. Amaro, and Ricky B. Nellas
Biophysical Journal, 120(3), p.299a

Computational reverse engineering of the lipase from Pseudomonas aeruginosa PAO1: α-helices
Adam Jo Elatico and Ricky Nellas
Journal of Molecular Graphics and Modelling, 100, p.107657

Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations
Corazon Ericka Mae Itang, Jokent Gaza, Dan Jethro Masacupan, Dessa Camille Batoctoy, Yu-Ju Chen, Ricky Nellas and Eizadora Yu
Marine drugs, 18(10), p.503

The interaction and mechanism of monoterpenes with tyramine receptor (SoTyrR) of rice weevil (Sitophilus oryzae)
Almira Ocampo, Mac Kevin Braza, and Ricky Nellas
SN Applied Sciences, 2, pp.1-9

Structural dynamics of neighboring water molecules of N-isopropylacrylamide pentamer
Kenee Kaiser Custodio, Gil Claudio, and Ricky Nellas
ACS omega, 5(3), pp.1408-1413

Potential Inhibitors of Galactofuranosyltransferase 2 (GlfT2): Molecular Docking, 3D-QSAR, and In Silico ADMETox Studies
Christopher Llynard Ortiz, Gladys Completo, Ruel Nacario, and Ricky Nellas
Scientific reports, 9(1), p.17096

Ligand-Induced Conformational Dynamics of A Tyramine Receptor from Sitophilus oryzae
Mac Kevin Braza, Jerrica Dominique Gazmen, Eizadora Yu, and Ricky Nellas
Scientific reports, 9(1), p.16275

Conformational dynamics of α-conotoxin PnIB in complex solvent systems
Jokent T. Gaza, Abdul-Rashid B. Sampaco III, Kenee Kaiser S. Custodio, and Ricky Nellas
Molecular Diversity, 24(4), pp.1291-1299

Machine learning for predicting electron transfer coupling
Chun-I Wang, Mac Kevin Braza, Gil Claudio, Ricky Nellas, Chao-Ping Hsu
The Journal of Physical Chemistry A, 123(36), pp.7792-7802

In silico insights on enhancing thermostability and activity of a plant fructosyltransferase from pachysandra terminalis via introduction of disulfide bridges
Christopher Llynard Ortiz, Hosea Matel, Ricky Nellas
Journal of Molecular Graphics and Modelling, 89, pp.250-260

Surface tension data of n-propane, n-octane and n-dodecane from nucleation simulations
Zamantha Nadir Martin, Imee Martinez, and Ricky Nellas
Tellus B: Chemical and Physical Meteorology, 70(1), pp.1-5

Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin
Remmer Salas, Jan Kathryne Garcia, Ana Carmela Miranda, Windell Rivera, Ricky Nellas, and Portia Mahal Sabido
Peptides, 104, pp.7-14

Molecular Affinity of Mabolo Extracts to an Octopamine Receptor of a Fruit Fly
Francoise Neil Dacanay, Ma. Carmina Joyce Ladra, Hiyas Junio, and Ricky Nellas
Molecules, 22(10), p.1677

DMSO enhanced conformational switch of an interfacial enzyme
Richard J. Lindsay, Quentin R. Johnson, Wilfredo Evangelista, Ricky B. Nellas, Tongye Shen
Biopolymers, 105(12), pp.864-872

The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor
Alexander K. Clark, J. Heath Wilder, Aaron W. Grayson, Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Elias J. Fernandez, Tongye Shen
The Journal of Physical Chemistry B, 120(33), pp.8338-8345

Pressure-induced conformational switch of an interfacial protein
Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Tongye Shen
Proteins: Structure, Function, and Bioinformatics, 84(6), pp.820-827

Mapping allostery through computational glycine scanning and correlation analysis of Residue–Residue contacts
Quentin R. Johnson, Richard J. Lindsay, Elias J. Fernandez, Ricky B. Nellas, Tongye Shen
Biochemistry, 54(7), pp.1534-1541

Effects of Branched O-Glycosylation on a Semiflexible Peptide Linker
Quentin R. Johnson, Richard J. Lindsay, Sherin R. Raval, Jeremy S. Dobbs, Ricky B. Nellas, Tongye Shen
The Journal of Physical Chemistry B, 118(8), pp.2050-2057

Nucleation Dynamics of Active Particles
Tongye Shen, Xianghong Qi, Ricky B. Nellas
The Journal of Physical Chemistry B, 117(42), pp.12844-12849

Solvent-Induced α- to 310-Helix Transition of an Amphiphilic Peptide
Ricky B. Nellas, Quentin R. Johnson, Tongye Shen
Biochemistry, 52(40), pp.7137-7144

Swimming motility plays a key role in the stochastic dynamics of cell clumping
Xianghong Qi, Ricky B Nellas, Matthew W Byrn, Matthew H Russell, Amber N Bible, Gladys Alexandre and Tongye Shen
Physical biology, 10(2), p.026005

Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa
Quentin R. Johnson, Ricky B. Nellas, Tongye Shen
Biochemistry, 51(31), pp.6238-6245

High-pressure effect on the dynamics of solvated peptides
Ricky B. Nellas; Mary M. Glover; Donald Hamelberg; Tongye Shen
The Journal of Chemical Physics, 136(14)

Stability and Sugar Recognition Ability of Ricin-like Carbohydrate Binding Domains
Jianzhuang Yao, Ricky B. Nellas, Mary M. Glover, Tongye Shen
Biochemistry, 50(19), pp.4097-4104

Exploring the discrepancies between experiment, theory, and simulation for the homogeneous gas-to-liquid nucleation of 1-pentanol
Ricky B. Nellas; Samuel J. Keasler; J. Ilja Siepmann; Bin Chen
The Journal of chemical physics, 132(16)

Fractal Aggregates in Protein Crystal Nucleation
Bin Chen, Ricky B. Nellas, Samuel J. Keasler
The Journal of Physical Chemistry B, 112(15), pp.4725-4730

An Aggregation-Volume-Bias Monte Carlo Investigation on the Condensation of a Lennard-Jones Vapor below the Triple Point and Crystal Nucleation in Cluster Systems:  An In-Depth Evaluation of the Classical Nucleation Theory
Bin Chen, Hyunmi Kim, Samuel J. Keasler, Ricky B. Nellas
The Journal of Physical Chemistry B, 112(13), pp.4067-4078

Molecular Content and Structure of Aqueous Organic Nanodroplets from the Vapor−Liquid Nucleation Study of the Water/n-Nonane/1-Alcohol Series
Ricky B. Nellas, Samuel J. Keasler, Bin Chen
The Journal of Physical Chemistry A, 112(13), pp.2930-2939

Towards understanding the nucleation mechanism for multi-component systems: an atomistic simulation of the ternary nucleation of water/n-nonane/1-butanol
Ricky B. Nellas, Bin Chen
Physical Chemistry Chemical Physics, 10(4), pp.506-514

Dumbbells and onions in ternary nucleation
Ricky B. Nellas, Bin Chen and J. Ilja Siepmann
Physical Chemistry Chemical Physics, 9(22), pp.2779-2781

Water mediated attraction between repulsive ions: A cluster-based simulation approach
Samuel J. Keasler; Ricky B. Nellas; Bin Chen
The Journal of chemical physics, 125(14)

Probing the Nucleation Mechanism for the Binary n-Nonane/1-Alcohol Series with Atomistic Simulations
Ricky B. Nellas, Matthew E. McKenzie, Bin Chen
The Journal of Physical Chemistry B, 110(37), pp.18619-18628

[6,6′-Bis­(chloro­meth­yl)-2,2′-bipyrid­yl]­dichloro­cobalt(II)
R. B. Nellas, F. R. Fronczek, G. R. Newkome, S. F. Watkins and Y. Xia
Acta Crystallographica Section E: Structure Reports Online, 62(7), pp.m1522-m1523