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Welcome to Parham Academy | Brief discription about the founder


Parham Jabbarzadeh Kaboli, PhD (in progress) in brief:

- A research leader in cancer discovery and cell signaling
- An experienced lecturer in cell and molecular biology
- An young investigator member of the European Association of Cancer Research (EACR)
- An associate member of the American Association of Cancer Research (AACR)
- A member of the American Society for Pharmacology and Experimental Therapeutics (ASPET)
- A member of the American Association for Advancement of Science (AAAS)

►Cellular & molecular pharmacologist
►Research scientist
►Expert in: Cell therapy/drug discovery/Data science
►Problem solver

Parham Jabbarzadeh Kaboli in detailed:

► CAREER PROFILE

• University Lecturer with management experience and exceptional people skills.
• Versed in laboratory tests and bioinformatics with focus on cell biology and cell-based assays.
• Desires a challenging role as a research scientist involving in drug discovery.
• Sale manager in pharmaceutical industry with background as reseller and consultant looking to join a growing entrepreneurial organization as part of the R&D team.

► PHD PROFILE

• Establishment of a virtual high-throughput screening platform to find out more suitable compounds compared with berberine which led to ONE innovation, SIX journal papers, ONE silver medal, and ONE governmental grant ($25000).
• Leading a team to develop virtual high-throughput screening platform (algorithm) by which thousands compounds can be automatically modeled against a specific target, and eventually binding efficiency index and ADMET parameters are predicted.

► COMMUNICATION

• Presenting research results at international scientific meetings in the UK and Italy held by British, European, and American associations for cancer research - BACR, EACR, and AACR respectively.
• Preparing PhD thesis (45,000 words) and annual progress report for grant awarding bodies.
• Teaching and demonstrating at undergraduate practical and tutorial sessions (2000-2013) and online training workshops (2011- present).
• NINE journal papers, FOUR conference papers, and TWO books have been authored which will be available upon request.

► INTERPERSONAL SKILLS

• Collaborating with colleagues to schedule and manage their needs in laboratories, and keeping in touch with suppliers.
• Supporting the development of new colleagues/lecturers through assisting with their professional training to ensure competence and personal safety.
• Recruiting and interviewing with new lecturers (2006-2013).

► CONTACT

parham@gromacs.net



Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
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Weekend Recipe for February 2016 - the fourth week

The birth of modern chemotherapy

This paper published in the Pharmacologist is very interesting showing you how chemotherapy has been evolved as a tool to treat cancer.


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Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
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Weekend Recipe for February 2016 - the second week

The impact of molecular dynamics on drug design: applications for the characterization of ligand– macromolecule complexes

This week I would like to suggest this paper. This paper is very great review paper which is useful for those are interested in drug discovery and are got a little bit confused.

Abstract——Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range.

The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand–protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.


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If interested in the field of drug discovery I would also like to suggest these articles. These are well-written too.

To download other weekend recipes click here.

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Each weekend, you are linked to the best article that , during each week, I have read and found it great in the field of Cancer and Pharmacology. I try to encourage the fellow researchers and post-graduate students to read so much as they can about new therapeutics.
-------------------------------------------

Weekend Recipe for February 2016 - the first week

Ligand efficiency indices for effective drug discovery

This week I would like to suggest this paper. This paper written by Prof. Cele Abad-Zapatero help me a lot to make new insights in drug discovery in my projects. The paper is incredibly insightful and provide new indices to better understanding of drug/target interaction.

Abstract——Successful drug discovery requires the optimization of a large number of variables ranging from strictly physicochemical parameters such as molecular weight to more complex parameters related to toxicity and bioavailability. Presently, structure-based methodologies influence many aspects of the drug discovery process from lead discovery to the final preclinical characterization. However, critical biological issues along the path to the market have diminished the impact and power of this methodology. The physicochemical properties of the novel chemical entities designed and guided by structural methods have become the subject of intense scrutiny from lead discovery to drug candidate. The idea of ligand efficiency (binding energy/non-hydrogen atoms) has recently emerged as a useful guide to optimize fragment and lead selection in the discovery process.

More generalized concepts of ligand efficiency, related to efficiency per dalton and per unit of polar surface area, have also been introduced and will be discussed in the broader context. Preliminary results and trends obtained using ligand efficiencies as guides are reviewed and their future application to guide drug discovery will be discussed, as well as their integration into the structure-based drug design methods to make them more effective and numerically robust.


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One of the objectives of this manuscript is studying of BRAF-MEK interaction.

Water systems were generated so that each docked protein was placed in the center of a triclinic box with the minimum distance between the solutes and the edge of the box of 1.0 nm. The size of the system is 286000 atoms. This system is a huge system and took one month for simulation.

BRAF-MEK1 complex docked by four molecules of BBR-9 can be seen here. Here, we have four BRAFs, four MEK1s, and four ligands. We have done MD to see whether BBR-9 affect BRAF-MEK1 interactions or not.

BBR-9 is one of our newly generated ligands against BRAF. I will also show that BBR-9 is a dual RAF inhibitor because it could affect CRAF as well.

After publication, article and all related supplimentary files will be available here.

RAF-MEK1

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Selected journal articles watson @ (11:59:34) (Curriculum Vitae)
Proofreading and Editing Service watson @ (14:10:53) (Services)
Our authorship guidline watson @ (13:06:25) (Weekend Recipe: For further reading)


Our article: Therapeutic miRNAs


 Pharmacological Research




Headlines





Date published: not known
Details

»Understanding the formation of spicules
»Lnc-ing fibroblasts to cardiac fibrosis
»Quantum effects in ambient conditions
»How to make a protein-based nanocontainer
»The influence of flying
»Instant tough bonding of hydrogels
»PKA-activation mechanism revised
»Optimum human input
»One person's meat is another's poison
»Broadening the immune spectrum


Date published: not known
Details

»Structure and Dynamics of the Liver Receptor Homolog 1-PGC1{alpha} Complex [Articles]
Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabo ...
»Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner [Articles]
The synthetic glucocorticoids (GCs) dexamethasone, mometasone furoate, and triamcinolone acetonide ...
»Novel Mode of Antagonist Binding in NMDA Receptors Revealed by the Crystal Structure of the GluN1-GluN2A Ligand-Binding Domain Complexed to NVP-AAM077 [Articles]
Competitive antagonists against N-methyl-D-aspartate (NMDA) receptors have played critical roles th ...
»Up-regulated Ectonucleotidases in Fas-Associated Death Domain Protein- and Receptor-Interacting Protein Kinase 1-Deficient Jurkat Leukemia Cells Counteract Extracellular ATP/AMP Accumulation via Pannexin-1 Channels during Chemotherapeutic Drug-Induced Apoptosis [Articles]
Pannexin-1 (Panx1) channels mediate the efflux of ATP and AMP from cancer cells in response to indu ...
»Negative Regulation of Human Pregnane X Receptor by MicroRNA-18a-5p: Evidence for Suppression of MicroRNA-18a-5p Expression by Rifampin and Rilpivirine [Articles]
Small noncoding microRNAs act as post-transcriptional regulators of gene expression involved in div ...
»Dexamethasone Downregulates Endothelin Receptors and Reduces Endothelin-Induced Production of Matrix Metalloproteinases in Cultured Rat Astrocytes [Articles]
In brain disorders, astrocytes change phenotype to reactive astrocytes and are involved in the indu ...
»A Glutamate-Substituted Mutant Mimics the Phosphorylated and Active Form of Guanylyl Cyclase-A [Articles]
Multisite phosphorylation is required for activation of guanylyl cyclase (GC)-A, also known as NPR- ...
»Molecular Basis of Metabolism-Mediated Conversion of PK11195 from an Antagonist to an Agonist of the Constitutive Androstane Receptor [Articles]
The constitutive androstane receptor (CAR) plays an important role in xenobiotic metabolism, energy ...
»Rapid Throughput Analysis of GABAA Receptor Subtype Modulators and Blockers Using DiSBAC1(3) Membrane Potential Red Dye [Articles]
Fluorometric imaging plate reader membrane potential dye (FMP-Red-Dye) is a proprietary tool for ba ...
»Correction to "The Orphan Receptor GPR17 Is Unresponsive to Uracil Nucleotides and Cysteinyl Leukotrienes" [ERRATUM]


Date published: not known
Details

»MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory
»NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
»Linking structure and activity in nonlinear spiking networks
»Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation
»Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression
»High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE
»A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images
»LASSIM—A network inference toolbox for genome-wide mechanistic modeling
»Transmembrane helical interactions in the CFTR channel pore
»Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities
»Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease
»Good enough practices in scientific computing


Date published: not known
Details


THE FOUNDER and CEO

Parham Jabbarzadeh Kaboli, PhD

Research scientist
in molecular medicine


Expert in:

Cell and molecular Biology
Modelling and drug discovery
Cancer signaling pathways

H-index= 3 (Google Scholar)
i10-index= 3
Overall ISI impact factor= 18.15
Overall citation= 110 (Google Scholar)

Memberships:

The American Society for Pharmacology and Experimental Therapeutics (ASPET)

American Association for Cancer Research (AACR)

European Association for Cancer Research (EACR)

American Association for Advancement of Science (AAAS)



CONTACT INFORMATION


Affiliation:
Department of Biomedical Science,
Faculty of Medicine and Health Sciences,
Universiti Putra Malaysia,
UPM Serdang 43400,
Selangor, Malaysia

E-Mail: parham@gromacs.net
Telegram: telegram.me/parhamacademy
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