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Questions related from Arvind Negi
I did a simple organic reaction where I left with excess of Polyhydroxymethylsiloxane (PHMS) in the final product solution. I tried to extract it with aqueous layer, but I failed. Let me know, if...
09 September 2015 2,819 3 View
I have a protein-protein complex and therefore, need a visualiser to look at those amino acids which are at interface of these proteins. However I am also interested to see the interactions...
07 July 2015 9,801 15 View
when we do superpose of 3 pdbs together (1 on 2, 2 on 3, 3 on 1) and after that if we change the sequence of superposition, will there be any possibility to see the change in RMSD value (before...
06 June 2015 8,159 7 View
Hi I am looking for a MD simulation calculations for Small molecule-Protein interaction. But right now I am limited to Windows. So please let me know if there is any software which is useful in...
11 November 2014 3,919 10 View
I want to dock a carbohydrate molecule as a ligand on a protein. What is the best scoring function/force field that I can use for this type of docking?
11 November 2014 3,207 5 View
I have 6 receptors and only 1 ligand. In the meantime I interested to do the docking in all these receptor. Is there any way where we have a generalised way to dock this compound to these receptor...
11 November 2014 4,507 12 View
I want to know about the tools available for searching for a protein or receptor for a known ligand.
10 October 2014 6,271 9 View
What we know is that the proteins get acetylated at lysine moiety. But looking into the structure, we got around more than one lysine moiety. Then how it can be possible to find out which lysine...
08 August 2014 1,213 6 View
What is the best reagent which can be useful in the reduction of 2,4-dinitrobenzaldeyde?
08 August 2014 1,860 16 View
Recently I was encountered with a problem where structure shown in figure is not able to get converted to any product. May be possibly due to its resonance effect or any other effect between the...
07 July 2014 1,663 18 View
Haddock Issue!!!! I wont able to find out how it works (Tutorial) in Protein protein interaction. After preparing both the proteins what is the next step?
06 June 2014 929 5 View
I have a protein of sequence of 1215 amino acids. As no 3D structure available, therefore I tried to build its homology model however there is a section of sequence which doesn't align to any...
05 May 2014 5,277 10 View
What are the conditions that favor the synthesis of triazole from hydrazone and nitrile?
04 April 2014 7,127 12 View
I want to know its synthetic route for any starting material which should be available.
04 April 2014 8,435 0 View
Recent reports clearly indicate that more than 70% of cancer cases, are caused by the bad habits. Those bad habits contain prominently alcohol consumption, tobacco and other things. But some...
02 February 2014 9,599 5 View
Is there any anticancer agent which induces apoptosis rather than inducing the necrosis as they usually do?
01 January 2014 8,357 13 View
Usually radiation pose the normal cell to mutate and extensively show other harmful effects, then how it can be better or have an edge over the chemotherapy?
01 January 2014 3,542 7 View
In cancer, the most awful situation after getting a chemotherapeutic agent, is its delivery. I heard about various vectors employed in their delivery. But is there any clinical or associated...
01 January 2014 3,060 4 View
In cancer, the tubulin is significant for sustaining the cell. Therefore researchers target it, but often only its beta subunit, not its alpha subunit.
01 January 2014 4,509 2 View
Usually Mitochondria and Chloroplast contain DNA, Can we called them gene. therefore I have asked this question.
12 December 2013 4,067 0 View
There are so many science magazines, which accept reviews as well as research articles. Does these magazines have impact factor?
12 December 2013 9,677 0 View
In tissue culture, I often see cells transforming due to unknown reasons even after taking precautions. More often seen during the seasonal changes. What are the possible ways of preventing...
12 December 2013 6,771 2 View
My question in the concern to evaluate the cellular transformation in the cell lines in a tissue culture lab?
12 December 2013 5,688 8 View
Usually nitrogen and argon environment is used during organic synthesis, but not the helium environment?
12 December 2013 3,762 9 View
Cancer cells usually have an acidic microenvironment. Is there any effect of the environment on the cancer cell survival or skipping the phagocytosis by the phagocytes?
12 December 2013 9,736 1 View
As most of chemotherapeutic agents against cancer improves longevity and standard of living in patient and still they are in progress of further development, however they can always related with...
12 December 2013 4,179 7 View
Usually cancer cells produce higher amount of lactate. But can it be useful for the cancer cells and how the cancer cells utilize the lactate?
12 December 2013 6,256 7 View
Cancer is heterogeneous diseases and it has extraordinary potential to survive even in adverse conditions (for e.g. hypoxia in the cancer cell). So its survival after these hurdles raises the...
12 December 2013 1,685 14 View
Recently I have seen in one of the article in New England Journal of Medicine that DPP-4 inhibitors or better to say "incretins based inhibitors" can increase the susceptibility towards cancer and...
12 December 2013 4,471 0 View
Tyrosine kinases utilizes the ATP for the phosphorylation during the normal intracellular signalling cascade, but it abruptly increases during the cancer progression. However this can be a better...
12 December 2013 5,997 1 View
Are there any drugs (especially anticancer drugs) known for their side effects in enhancing the progression of cancer (or inducing a cancer in other cells of different origin of the body). My...
12 December 2013 4,620 15 View
Here I attached a snap shot of my data.
12 December 2013 1,822 13 View
For docking studies we usually take nascent protein and after receptor preparation, we dock the energy minimized ligand. Meantime we also need to choose the docking site and what if we choose a...
12 December 2013 7,528 1 View
CH3F, CH3Cl, CH3Br, CH3I.
12 December 2013 1,787 7 View
Suppose we have 3 structurally similar ligands and we performed docking via 2 different algorithms of the same software. Is there any way to apply Bio-stats on the results?
12 December 2013 2,241 5 View
If anyone knows about these terminologies please let me know! Binding energy, Ligand efficiency, Inhibition constant (µM), Inter molecular energy, Vander Waals desolvation energy, Electrostatic...
12 December 2013 6,010 5 View
I need a molecular dynamics freeware.
11 November 2013 8,638 1 View
Normally Hb carries 4 oxygen atoms, but is there any condition where it carries more than 4?
11 November 2013 4,611 0 View
Excess of hippuric acid is manifested by which disease or which organ or body part associated malfunctioning.
11 November 2013 268 1 View
Parasite need host for its survival and to regulate its life cycle. Since last some decade we are fortunate to find out the novel target in their metabolism which are absent in human. And mainly...
11 November 2013 805 1 View
Orphan receptor are those receptors which don't have their endogenous ligands in the body. But still these are present in our body. What is their physiological role in our body?
11 November 2013 3,928 10 View
Conserve amino acid of conserved domain show conserved interaction with their substrate. Can there be a chance of probability of conserve amino acid mutation, as moving from one species to other...
11 November 2013 9,788 0 View
Topology prediction is a bioinformatics tool which assist in mapping the surface of the functional protein. Which software imparts the best topology prediction?
11 November 2013 8,436 2 View
Homology modelling is the type of comparative - template based modelling. What can be the structure that homology modelling estimate - Primary, secondary, tertiary and quaternary.
11 November 2013 9,665 4 View
Normally we use AMBER and CHARMM for protein minimization. Can anyone tell me which one is better AMBER or CHARMM?
11 November 2013 3,381 4 View
Insulin, like growth factor receptor-1 (IGF-1R) is well characterized in cancer and there are lots of clinical agents in preclinical development phase, but still there is no drug or no clinical...
11 November 2013 2,029 2 View
We know the insulin more as metabolic hormone but recently i read a news published in nature supplement about its role in immunity. can i get more information in this concern.
11 November 2013 10,107 8 View
Nanotechnology is advanced technology which makes a new interface in drug designing. Still it is in its developing phase. But through this question, I want to know about the current status of...
11 November 2013 1,870 8 View
Cancer shows lowered pH, what does this indicate and why cancer cell prefer to do this? Is anything relevant or edge that it can get after making the acidic micro-environment?
11 November 2013 1,063 21 View
Autophagy is self-phagocytosis and apoptosis is self-killing. But these processes are regulated in the normal cell and in the cancer cell.
11 November 2013 5,952 0 View
Usually I have seen journal aims and scope possessing research articles, reviews, focus, perspectives and commentaries. What are these commentaries and what data is required in it to publish?
11 November 2013 2,566 4 View
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11 November 2013 1,361 4 View
Cancerous cells dysfunction in aerobic respiration (i.e. TCA cycle, which provides energy to normal cells), therefore in search of energy, cancerous cells plan to reprogram their energy...
11 November 2013 9,950 0 View
Cancer is genetic metabolic disorder, untreatable and can be fatal. Whereas the cancerous cells are different from the normal cells. But what is driving force which switch a normal cell to...
11 November 2013 6,301 2 View
Cancer has 8 different hallmarks and heterogeneous in nature. Which type of signalling in cancer only happens in advance stages of cancer?
11 November 2013 7,199 36 View
Usually we read these terminologies quite often. But where they can be useful is still be problematic as before we don't know their proper meaning.
11 November 2013 9,269 4 View
Insulin has well characterized as metabolic hormone, moreover also identified for mitogenic effects. Because of mitogenic nature of insulin, it is quite curious to know that in the development of...
11 November 2013 5,457 2 View
Bonding can be crucial in the biological system for proper orientation of a molecule. Can we estimate or characterize the bonding via ab-initio calculations?
11 November 2013 2,693 14 View
Pie-pie interactions are the kind of weak interaction. Is there any method to characterize these interaction via ab-initio calculation?
11 November 2013 5,424 3 View
Splicing an insulin gene results in two isoforms of the insulin receptor, A and B, where A implicates a mitogenic effect and B a metabolic effect. But for the mitogenic effect, IGF-1R is present...
11 November 2013 6,138 1 View
Insulin receptor signalling contains phosphorylation cascade initiates transphoporylation or autophosphorylation or both? Please suggest the type of phosphorylation it follows
11 November 2013 3,049 0 View
Allosteric binding sites are different from the active sites. If insulin receptor has this characteristic then it will be easy to target the receptor in insulin associated disorders.
11 November 2013 4,314 0 View
Recently the role of telomerase was identified in cancer.
11 November 2013 8,171 4 View
Virtual screening in autodock need single file of ligands which comprises the number of ligands needed to be docked. I am unable to form a single file of ligands.
11 November 2013 7,735 1 View
Topology prediction is a bioinformatics tool which assist in mapping the surface of the functional protein. But normally this functional protein is membrane protein. Why we can't do the topology...
11 November 2013 8,356 3 View
Usually in modelling software we have the option to map the surface either electrostatically or hydrophobically. How are they different and how can they be beneficial in biological systems?
11 November 2013 5,949 0 View
I took a pdb from protein data bank and extract the ligand and docked it, on the same pdb. My RMSD value was found to be 0.569 which is under the permissible limit. As such this is used to...
11 November 2013 211 9 View
I need to see hybrid receptor formation and their interaction.
11 November 2013 7,021 0 View
I am looking into the use of a lentiviral vector in targeting of different diseases.
11 November 2013 8,032 0 View
Viruses are nucleoproteins and they are useful in drug delivery but can they be helpful in transmitting the area of interest gene to the receiver?
11 November 2013 6,265 1 View
Recently histamine-3 receptor was discovered but its physiological role is unknown. Is there any report related to this concern?
Dolichol phosphatase is a unique enzyme in carbohydrate metabolism. It also causes glycosylation of the protein. Any suggestion will be helpful.
11 November 2013 7,486 2 View
Liver on right, pancreas on left, spleen on left, etc, why this orientation is only preferred! and why is it always likely to have for all human body. Is there any report or case where this...
11 November 2013 6,947 0 View
Usually ATP does the phosphorylation , but is there any other energy molecule which can phosphorylate.
11 November 2013 5,844 0 View
Like blue color of CUSO4, various salts have different colors. Why is this so and some salts have different colors?
11 November 2013 2,271 3 View
I am preparing chalcone where the reactants for chalcone preparation are 2-hydroxy-benzaldehyde and 2-amino-acetophenone. Is there a way to synthesize a chalcone from these reactants?
11 November 2013 4,818 7 View
Usually we hear it called the brain tumor but why can't we say they are cancerous cells. Is this because their lack of metastasis. Why is it so?
11 November 2013 8,162 12 View
M.pharm students have different studies which are different from the the course studies in life sciences, chemical sciences and any other sciences. Therefore it makes atypical for pharmacy...
11 November 2013 2,001 3 View
Migraine is the persistent pain in the head for long time.
10 October 2013 5,660 0 View
Cancer is a metabolic disorder which is fatal and it is caused by the complex signalling of different receptors. There are mainly 4 types of receptors and they must have a dominant role in...
10 October 2013 3,240 1 View
Human Leukocyte antigen G has been discovered recently and also found its role in cancer but how is it beneficial to anticancer therapy?
10 October 2013 7,560 2 View
Normally MTT assay is used for evaluating the anticancer activity of synthesize compounds. How much MTT is reliable?
10 October 2013 8,267 16 View
I am working on the sulfur metabolism and if I want to isolate a protein from the cytoplasm, which would be the best method to isolate the protein?
10 October 2013 7,453 3 View
Usually we can prepare homology model, but problem comes in their evlaution. What are various ways to evaluate the homology model?
10 October 2013 4,785 7 View
Normally in cancer the number of surface receptors increases and, with that, hybridization also occurs. But does it have a role in cancer proliferation?
10 October 2013 4,582 2 View
I am trying to find out about the possible resistance for kinase inhibitor in cancer?
10 October 2013 1,288 12 View
Thalidomide is drug that did 1960 thalidoamide disaster and banned then after. But now it come again and presebnt in clinical development for anticancer chemotherapy
10 October 2013 1,138 1 View
Dendritic cells are usually inactive in state. But can be activated in some pathological conditions.
10 October 2013 5,389 39 View
Insulin is the first polypeptide hormone discovered. But it still doesn't have an antagonist?
10 October 2013 7,006 3 View
Now-a-days, I often heard about the COX-2 inhibitors are being used in cancer. But as my best of knowledge I know that they are useful in inflammatory conditions.
10 October 2013 1,376 6 View
Recently some reports were indicating the paracetamol as anticancer agent and also suggested the mechanism via the same route as the aspirin do. Any suggestion?
10 October 2013 3,154 2 View
Seeking advice on the subject.
10 October 2013 6,782 3 View
I am trying to do flexible docking, but I am unable to do so. Is there any protocol or proper manual to assist me.
10 October 2013 9,924 0 View
What are the different ways to evaluate a loop in a homology modelor loop modelling?
10 October 2013 1,009 1 View
Online software to make the phylogentic tree on the basis of the amino acid sequence of novel protein.
10 October 2013 7,548 2 View
Techniques which are accompanied to isolate a enzyme from the cytolpasm
10 October 2013 8,293 2 View
Normally patient are dripped with 0.9% NaCl. Is there any other salt or its conc. Which replace the traditional way.
10 October 2013 5,402 7 View
Is there a method which can be used to estimate uranium in water. Any suggestions will be helpful.
10 October 2013 1,351 23 View
Chalcone synthesis.
10 October 2013 685 3 View
Insulin Receptor and IGF-1R are structural homologous to each other therefore their ligands share common signalling but the selectivity is only possible when we they better understanding of their...
10 October 2013 8,559 0 View
Normally cancer cell utilize anaerobic respiration so why are researchers more focused on isocitrate dehydrogenase (ISH)? ISH is a penultimate enzyme of Kreb cycle (TCA), which works on aerobic...
10 October 2013 639 0 View
Telomerase in cancer.
10 October 2013 408 3 View
I read in Mangan et al 2004, that helminth infection protect from the anaphylaxis shock. That indicate that the other worm infection can also be beneficial in case of anaphylaxis shock. Is it so?
10 October 2013 4,262 1 View
Sickle cell anemia is a disorder of RBC, where their shape disrupt. But how it assist to the person to develop the resistance towards to the malaria.
10 October 2013 5,350 3 View
Drugs either bind to the substrate or cofactor binding site but which one is better to target?
09 September 2013 2,960 6 View
Normally inhibition possibly can be differentiate into various category but when you go through different books or articles sometimes we get confused in these terminologies
09 September 2013 5,815 13 View
Substituents like 4-cl, 4-OH, 3,5-Dichloro, 2,5-Dmethoxy on the benzylamine ring
09 September 2013 9,779 2 View
MM2 force field system minimise the small molecules of organic chemistry which contains different substituents like nitro, OH, Cl, (3, 5-Dichlro), OCH3 etc. How can we purpose which has higher and...
09 September 2013 5,159 1 View
Both 2-OH-benzylamine or 2-NO2-benzylamine have similar structure except the substitution. What is the possible/predictable reason to have high or low Non-1,4 van der Waals (Non-1,4 VDW) energy...
09 September 2013 8,486 0 View
Is steric hindrance increases the Non-1,4 VDW energy or not?
09 September 2013 4,519 0 View
Is there any particular protocol to follow for this kind of assay?
09 September 2013 2,143 2 View
Gamma GT is utilized as liver function test. One patient was diagnosed with lower level of gamma GT. What can be inferred by the lowering level of gamma GT
09 September 2013 5,822 0 View
Why does the spleen become enlarged during malaria?
09 September 2013 2,431 12 View
Citrus fruits are the source of citric acid and many times I heard people saying that they eat citrus fruit as a better supplement for vitamin C.
09 September 2013 3,768 3 View
Is it the same or a different meaning of these terms?
09 September 2013 902 7 View
RBC doesn't have a nucleus so is there any exception virus which can affect the RBC?
09 September 2013 5,259 5 View
Before maturity they possess nucleus but after maturity they lose it, why?
09 September 2013 6,638 23 View
Higher affinity for CO induce suffocation which may be fatal.
09 September 2013 5,202 6 View
Antagonist and inhibitor difference
09 September 2013 1,536 13 View
Interactions can be any kind.
09 September 2013 9,371 3 View
Every cell needs energy which comes from glucose. If we apply this cellular property then, can we say that the glucose proliferate cancer cells?
09 September 2013 8,814 6 View
I often encountered both these term, when I was reading a chapter in biochemistry.
09 September 2013 6,603 11 View
Cancer is a metabolic disorder which is fatal and there is no cure to treat this demon.
09 September 2013 6,340 2 View
APE repairing enzyme, a druggable target.
09 September 2013 5,938 1 View
Why are sea snakes usually more poisonous than terrestrial snakes?
09 September 2013 2,079 1 View
Pie-pie interaction of aromatic ring systems is unique in nature and can be affected by the substitution on the rings.
09 September 2013 2,563 1 View
Why not the other size?
09 September 2013 7,331 2 View
Human body consist of around 90 tyrosine kinases. If one tries to target them selectively then what are the factors or measure he/she must be carefully employed? For instance, if a inhibitor is...
09 September 2013 3,487 7 View
Repairing enzyme APE has two terminals: C-terminal and N-terminal. Now the role of APE repair enzyme is well characterized but its both terminal participate in cancer progression. So which one is...
09 September 2013 3,366 1 View
Hypoxia is one of the governing factors which cause cancer cell to proliferate.
09 September 2013 8,970 2 View
Recently role of APE repair enzyme was discovered and now it is more likely to ask this question. How much it has expression in the cancer?
09 September 2013 3,502 1 View
C-terminal of APE enzyme involve in repairing of DNA while N-terminal in redox activation of transcription factors. Is there any report when both terminals work together in signalling or come...
09 September 2013 9,148 4 View
What is the role of Isocitrate dehydrogenase in leukemia?
09 September 2013 2,473 1 View
Denaturation of protein is easy, but can we restore the functional structure of protein again?
09 September 2013 5,709 2 View
Which is the best online energy minimizing software for proteins?
09 September 2013 7,605 2 View
There are so many softwares for docking but which one is best? On which we have to rely?
09 September 2013 3,707 2 View
I want to know how substitutions like 2-NO2, 4-Cl, 4-OH, 3,4-dimethoxy, change the dipole-dipole steric interaction?
09 September 2013 5,879 2 View
I heard about the alanine scanning mutagenesis but not the other amino acid mutagenesis. Is there any specialty in alanine?
09 September 2013 2,161 3 View
Cystathionine is a sulphur containing precursor used for the biosynthesis of different sulfur containing metabolite.
09 September 2013 5,283 3 View
Difference between medicinal, pharmaceutical, clinical and Medicinal Biochemistry
09 September 2013 4,309 5 View
Can we estimate E-Z configuration using infrared spectroscopy?
09 September 2013 1,632 6 View
What is the best way to find the configuration of imine in a compound?
09 September 2013 308 1 View
09 September 2013 7,001 0 View
09 September 2013 1,236 0 View
Reactant is 5-amino-4-cyano-imidazole ring, tried so many methods but yet can't get any success. I tried around 37 methods to get tetrazole but if u will draw the structure you will find the...
09 September 2013 9,584 7 View
09 September 2013 7,439 2 View
Tyrosine kinase (TK) are essential components in humans and their role has been manifested in many diseases. Normally we used to synthesise the TK inhibitors. So I want to know is there any plant...
09 September 2013 6,805 3 View
Forcefield used to minimise protein energy
09 September 2013 9,298 4 View
Homology modelling at low alignment
08 August 2013 5,525 17 View
