Umesh PanwarAlagappa University · Department of Bioinformatics
Umesh Panwar
Ph.D.
About
25
Publications
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Introduction
Umesh Panwar currently works at the Department of Bioinformatics, Alagappa University. Umesh does research in Bioinformatics, Computational Drug Designing on viruses, and also programming. Their current project is 'Computational Drug Discovery'.
Publications
Publications (25)
Background
The current study recognizes the significance of estrogen receptor alpha (ERα) as a member of the nuclear receptor protein family, which holds a central role in the pathophysiology of breast cancer. ERα serves as a valuable prognostic marker, with its established relevance in predicting disease outcomes and treatment responses.
Method
I...
Cheminformatics and its role in drug discovery is expected to be the privileged approach in handling large number of chemical datasets. This approach contributes toward the pharmaceutical development and assessment of chemical compounds at a faster rate efficiently. Additionally, as technological advancement impacts research, cheminformatics is bei...
Due to its capacity to drastically cut the cost and time necessary for experimental screening of compounds, virtual screening (VS) has grown to be a crucial component of drug discovery and development. VS is a computational method used in drug design to identify potential drugs from enormous libraries of chemicals. This approach makes use of molecu...
Glioblastoma (GBM) is a WHO Grade IV tumor with poor visibility, a high risk of comorbidity, and exhibit limited treatment options. Resurfacing from second-rate glioma was originally classified as either mandatory or optional. Recent interest in personalized medicine has motivated research toward biomarker stratification-based individualized illnes...
Secretory proteins play an important role in the tumor microenvironment and are widely distributed throughout tumor tissues. Tumor cells secrete a protein that mediates communication between tumor cells and stromal cells, thereby controlling tumor growth and affecting the success of cancer treatments in the clinic. The cancer secretome is produced...
Glioblastoma (GBM) is a WHO Grade IV tumor with poor visibility, a high risk of comorbidity, and limited treatment options. Resurfacing from second-rate glioma was originally classified as either mandatory or optional. Recent interest in personalized medicine has motivated research toward biomarker stratification-based individualized illness therap...
Estrogen receptor alpha (ERα), a nuclear receptor protein encoded by the estrogen receptor1 (ESR1) gene, is an important biomarker in breast cancer diagnosis. Any dysregulation in its expression can actively implicate the development and progression of the disease. ERα is abnormally expressed in around 60% of the active cases, making it an importan...
Estrogen receptor alpha (ERα), a nuclear receptor protein encoded by the estrogen receptor1 (ESR1) gene, is an important biomarker in breast cancer diagnosis. Any dysregulation in its expression can actively implicate the development and progression of the disease. ERα is abnormally expressed in around 60% of the active cases, making it an importan...
The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integra...
Flaviviridae is an enveloped viruses composed of positive sense single stranded RNA genome. Flaviviruses causes a major outbreak around the globe through the allegation of life threatening diseases with strident risk to death. Every year, people around the globe reports for the victim of various diseases like Dengue fever, Yellow fever, Encephaliti...
Since HIV-1 integrase makes use of host genome machinery to accomplish the replication process, where LEDGF/p75 (a cellular cofactor) executes in the lentiviral integration process by interacting with integrase. Thus, the integrase-LEDGF/p75 interaction has become an interesting drug target in developing a potent agent. The purpose of the present s...
The recent pandemic outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), raised global health and economic concerns. Phylogenetically, SARS-CoV-2 is closely related to SARS-CoV, and both encode the enzyme main protease (Mpro/3CLpro), which can be a potential target inhibiting viral replication. Through this...
SARS-CoV-2 encodes the Mac1 domain within the large non-structural-protein 3, which has an ADP-ribosylhydrolase activity conserved in other coronaviruses. ADP-ribosylhydrolase activity of Mac1 makes it an essential virulence factor for the pathogenicity of CoV. They have a regulatory role in counteracting host-mediated antiviral ADP-ribosylation, w...
Background
The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases has overwhelmed health and public health services. AI and ML algorithms have extended its major role in tracking the disease patterns, and in identifying possible treatment of disease.
Objective
To identify potential COVID-19 proteas...
Bacteriophages are considered to be the small viruses possessing an important role to infect bacteria’s tending to replicate therefore maintaining the environment of bacteria existence in equilibrium. Bacteriophages were considered to be potent therapeutics for the treatment against the bacterial infections in humans. Initially, bacteriophages were...
The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) calls the whole world into a medical emergency. For tackling Coronavirus Disease 2019 (COVID-19), researchers from around the world are swiftly working on designing and identifying inhibitors against all possible viral key protein targets. One of the attracti...
High risk human papillomaviruses are highly associated with the cervical carcinoma and the other genital tumors. Development of cervical cancer passes through the multistep process initiated from benign cyst to increasingly severe premalignant dysplastic lesions in an epithelium. Replication of this virus occurs in the fatal differentiating epithel...
Background
Today, HIV-1 infection has become an extensive problem to public health and a greater challenge to all working researchers throughout the world. Since the beginning of HIV-1 virus, several antiviral therapeutic agents have been developed at various stages to combat HIV-1 infection. But, the many of antiviral drugs are on the platform of...
Background:
Obesity is well known multifactorial disorder towards the public health concern in front of the world. Increasing rates of obesity has characterized with liver diseases, chronic diseases, diabetes mellitus, hypertension, and stroke, hearts improper function, reproductive and gastrointestinal, gallstones. An essential enzyme pancreatic...
Today, the world’s most difficult task is to improve the human health in the form of potential and functional efficiency. Therefore, synthetic biology is an emerging approach of medicinal science which is now on the edge of creating a novel life with potential and effective functions at genetic level. It represents the responsibility of engineering...
De novo design technique is complementary to high-throughput virtual screening and is believed to contribute in pharmaceutical development of novel drugs with desired properties at a very low cost and time-efficient manner. In this chapter, we outline the basic de novo design concepts based on computational methods with an example.
Rapidly increasing emergence of drug resistance has
become a wide-reaching challenge to combat latent
viral infection in recent years. HIV-1 virus is a
causative agent of AIDS, has cost millions of lives
across the world in last two decades. As, the genome
organization of HIV-1 virus consist of three essential
viral enzymes Reverse transcriptase, P...
HIV -1 integrase is a unique promising component of the viral replication cycle, catalyzing the integration of reverse transcribed viral cDNA into the host cell genome. Generally, IN activity requires both viral as well as a cellular co-factor in the processing replication cycle. Among them, the human lens epithelium-derived growth factor (LEDGF/p7...
Objective:
The purpose of the review is to portray the theoretical concept on neurological disorders from research data.
Background:
The freak changes in chemical response of nerve impulse causes neurological disorders. The research evidence of the effort done in the older history suggests that the biological drug targets and their effective fea...
Questions
Questions (8)
As I have to convert gromacs xtc into DCD formats for some analysis using Bio3D. Does anyone have the mdtools catdcd (https://www.ks.uiuc.edu/Development/MDTools/catdcd/)? Kindly please share with me through google drive or drop box?
Note: Any alternative solution for conversion of xtc into dcd ? That also will be fine.
I will be thankful to you.
Umesh Panwar
Kindly suggest some freely available softwares to calculate the HOMO/LUMO/MESP?
AS, I have run 100 ns simulation in desmond on protein-ligand complex. Can anyone help me out to converting the desmond trajectories into gromacs, thus i can further perform pca analysis.
Thanks for the support and help.
While running the command getting following error given below:
do_dssp -s md.tpr -f md.xtc
Fatal error:
Not enough memory. Failed to calloc -1082130432 elements of size 4 for grps[j].nm_ind
NVT steps Command : gmx grompp -f NVT.mdp -c EM.gro -p topol.top -n index.ndx -o nvt.tpr
Error:
Fatal error:
[ file strong_posre_make_ligand.itp, line 5 ]:
Atom index (4579) in position_restraints out of bounds (1-43).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Please help me out for this issue. I will be thankful to you.
Here is my problem:
(1) a peptide about 10 amino acids
(2) target protein (an enzyme with known PDB structure file, and known active sites)
(3) how to find the most reliable binding site and the complex structure? (also need result like free energy)
Thank you!!!
Dear All,
In a peptide (from Histone 3 ), on the 9th/14th position of Lysine we have done acetylation. Now, I have to run a simulation but I don't have force field parameters for acetylated Lysine residue. So, I would like to request, if anyone have any idea please suggest or if someone has the parameters for acetylated Lysine residue please send me the file. Thanking you.
Does anyone have any idea about how to convert linear peptide into cyclic peptide using Bioinformatics tool?
Thanks and Regards.
