- Singapore
- Nanyang Technological University, School of Computer Engineering, Graduate Studentadd
Research Interests:
Research Interests:
Early-stage drug discovery has been limited by initial hit identification and lead optimization and their associated costs (1). Ultra-large virtual screens (ULVSs), which involve the virtual evaluation of massive numbers of molecules to... more
Early-stage drug discovery has been limited by initial hit identification and lead optimization and their associated costs (1). Ultra-large virtual screens (ULVSs), which involve the virtual evaluation of massive numbers of molecules to engage a macromolec-ular target, have the ability to significantly alleviate these problems, as was recently demonstrated in multiple studies (2–7). Despite their potential, ULVSs have so far only explored a tiny fraction of the chemical space and of available docking programs. Here, we present VirtualFlow 2.0, the next generation of the first open-source drug discovery platform dedicated to ultra-large virtual screen ings. VirtualFlow 2.0 provides the REAL Space from Enamine containing 69 billion drug-like molecules in a "ready-to-dock" format, the largest library of its kind available to date. We provide an 18-dimensional matrix for intuitive exploration of the library through a web interface, where each dimension corresponds to a molecul...
Research Interests:
Clinical gait analysis is an important biomechanics field that is often influenced by subjectivity in time-varying analysis leading to type I and II errors. Statistical Parametric Mapping can operate on all time-varying joint dynamics... more
Clinical gait analysis is an important biomechanics field that is often influenced by subjectivity in time-varying analysis leading to type I and II errors. Statistical Parametric Mapping can operate on all time-varying joint dynamics simultaneously, thereby overcoming subjectivity errors. We present MovementRx, the first gait analysis modelling application that correctly models the deviations of joints kinematics and kinetics both in 3 and 1 degrees of freedom; presented with easy-to-understand color maps for clinicians with limited statistical training. MovementRx is a python-based versatile GUI-enabled movement analysis decision support system, that provides a holistic view of all lower limb joints fundamental to the kinematic/kinetic chain related to functional gait. The user can cascade the view from single 3D multivariate result down to specific single joint individual 1D scalar movement component in a simple, coherent, objective, and visually intuitive manner. We highlight MovementRx benefit by presenting a case-study of a right knee osteoarthritis (OA) patient with otherwise undetected postintervention contralateral OA predisposition. MovementRx detected elevated frontal plane moments of the patient's unaffected knee. The patient also revealed a surprising adverse compensation to the contralateral limb. Abbreviations CLI Command line interface GUI Graphical user interface SPM Statistical parametric mapping SPM1D One-dimensional statistical parametric mapping TKR Total knee replacement
SPM is a statistical method of analysis of time-varying human movement gait signal, depending on the random field theory (RFT). MovementRx is our inhouse-developed decision-support system that depends on SPM1D Python implementation of the... more
SPM is a statistical method of analysis of time-varying human movement gait signal, depending on the random field theory (RFT). MovementRx is our inhouse-developed decision-support system that depends on SPM1D Python implementation of the SPM (spm1d.org). We present the potential application of MovementRx in the prediction of increased joint forces with the possibility to predispose to osteoarthritis in a sample of post-surgical Transtibial Amputation (TTA) patients who were ambulant in the community. We captured the three-dimensional movement profile of 12 males with TTA and studied them using MovementRx, employing the SPM1D Python library to quantify the deviation(s) they have from our corresponding reference data, using “Hotelling 2” and “T test 2” statistics for the 3D movement vectors of the 3 main lower limb joints (hip, knee, and ankle) and their nine respective components (3 joints × 3 dimensions), respectively. MovementRx results visually demonstrated a clear distinction in...
Research Interests:
This is code of paper proposed a framework based on a wrapper selection approach for features selection in Ligand based virtual screening. It consists of an optimizer, Gradient-Based Optimizer (GBO), that hybridized with the classifier,... more
This is code of paper proposed a framework based on a wrapper selection approach for features selection in Ligand based virtual screening. It consists of an optimizer, Gradient-Based Optimizer (GBO), that hybridized with the classifier, k-nearest neighbor (k-NN). The performance of the introduced framework, GBO-KNN,
Research Interests:
Research Interests:
SARS-CoV-2 is a newly emerged coronavirus that causes a respiratory disease with variable severity and fatal consequences. It was first reported in Wuhan and subsequently caused a global pandemic. The viral spike protein binds with the... more
SARS-CoV-2 is a newly emerged coronavirus that causes a respiratory disease with variable severity and fatal consequences. It was first reported in Wuhan and subsequently caused a global pandemic. The viral spike protein binds with the ACE-2 cell surface receptor for entry, while TMPRSS2 triggers its membrane fusion. In addition, RNA dependent RNA polymerase (RdRp), 3′–5′ exoribonuclease (nsp14), viral proteases, N, and M proteins are important in different stages of viral replication. Accordingly, they are attractive targets for different antiviral therapeutic agents. Although many antiviral agents have been used in different clinical trials and included in different treatment protocols, the mode of action against SARS-CoV-2 is still not fully understood. Different potential repurposed drugs, including, chloroquine, hydroxychloroquine, ivermectin, remdesivir, and favipiravir, were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target prote...
Research Interests:
SARS-CoV-2 is a newly emerged coronavirus that causes a respiratory disease with variable severity and fatal consequences. It was first reported in Wuhan and subsequently caused a global pandemic. The viral spike protein binds with the... more
SARS-CoV-2 is a newly emerged coronavirus that causes a respiratory disease with variable severity and fatal consequences. It was first reported in Wuhan and subsequently caused a global pandemic. The viral spike protein binds with the ACE-2 cell surface receptor for entry, while TMPRSS2 triggers its membrane fusion. In addition, RNA dependent RNA polymerase (RdRp), 3-5 exoribonuclease (nsp14), viral proteases, N, and M proteins are important in different stages of viral replication. Accordingly, they are attractive targets for different antiviral therapeutic agents. Although many antiviral agents have been used in different clinical trials and included in different treatment protocols, the mode of action against SARS-CoV-2 is still not fully understood. Different potential repurposed drugs, including, chloroquine, hydroxychloroquine, ivermectin, remdesivir, and favipiravir, were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target protein...
Research Interests:
Background: Clinical gait analysis is an important field of biomechanics that Is influenced by subjectivity, which can lead to type I and II errors. Statistical Parametric Mapping (SPM) is a classical hypothesis testing method that can... more
Background: Clinical gait analysis is an important field of biomechanics that Is influenced by subjectivity, which can lead to type I and II errors. Statistical Parametric Mapping (SPM) is a classical hypothesis testing method that can operate on all measured joint dynamics simultaneously, thereby overcoming errors associated with subjective reduction of these complex data and providing a quantitative and coherent assessment. Results: We present MovementRx, the first gait analysis modelling application that models joints in 3 degrees of freedom. It is a python-based versatile GUI-based movement analysis decision support system, that provides a holistic view of all lower limb joints fundamental to the kinematic/kinetic chain (i.e., related to functional gait). It utilizes the time varying statistical tool SPM1D combined with a visualizing software. The user can cascade the view from single 3D multivariate result down to specific single joint individual scalar component of movement in...
Research Interests:
Research Interests:
“Virtual Screening” is a common step of in silico drug design, where researchers screen a large library of small molecules (ligands) for interesting hits, in a process known as “Docking”. However, docking is a computationally intensive... more
“Virtual Screening” is a common step of in silico drug design, where researchers screen a large library of small molecules (ligands) for interesting hits, in a process known as “Docking”. However, docking is a computationally intensive and time-consuming process, usually restricted to small size binding sites (pockets) and small number of interacting residues. When the target site is not known (blind docking), researchers split the docking box into multiple boxes, or repeat the search several times using different seeds, and then merge the results manually. Otherwise, the search time becomes impractically long. In this research, we studied the relation between the search progression and Average Sum of Proximity relative Frequencies (ASoF) of searching threads, which is closely related to the search speed and accuracy. A new inter-process spatio-temporal integration method is employed in Quick Vina 2, resulting in a new docking tool, QuickVina-W, a suitable tool for “blind docking”, (not limited in search space size or number of residues). QuickVina-W is faster than Quick Vina 2, yet better than AutoDock Vina. It should allow researchers to screen huge ligand libraries virtually, in practically short time and with high accuracy without the need to define a target pocket beforehand.