Structural Bioinformatics and Structural Biology - Science topic

I have been a little concerned that the 7H9 media for growing mycobacteria becomes cloudy and crashes out of solution after autoclaving. It is fully dissolved before autoclaving and is clear, but once it has been autoclaved a sandy precipitate accumulates at the bottom of the bottle. Is this a standard problem? Is there anything we can do?

Hey, I have been trying to design a peptide for a surface receptor using the RF-diffusion, But every time I am getting a peptide that has only glycine as the residue in results. I have looked at multiple literature but could not find relevant explanation.

I am currently learning about PyMol to utilize in my project. I used PyMol to visualize potential H-bond interactions in specific amino acid residues. However, I have discovered that Arg465 and Ser461 show a distinct interaction, as shown.

Please help identify this interaction.

I am docking multiple ligands (new designed ligand) against my protein using Autodock Vina in Chimera. The results displayed in this program are somewhat strange, because in some cases the ligands with no hydrogen bond or fewer bonds has the most negative Score than the ligand with more hydrogen bonds!!? Please look at the picture to get my mean(The best model in ligand with 2 hydrogen bonds has a score -8.3, While the best model in ligand with one or zero hydrogen bond has score -8.7 and -10.1 respectively!).

I understand that checking with other software or tools like PyMOL or PDBSUM will better help to analyze the possible interactions, however since I have several ligands with almost similar score and interaction network or equal hydrogen bond numbers, I am curious to now how to pick the best one (based on the in silico analysis) among them. If any body has suggestion for this I will appreciated it.

What to do if ChimeraX software doesn't recognise the .chimerax file downloaded from SwissDock after docking?

Besides, the zip file of prediction done was empty.

Thank you.

I want to cluster multiple pdb files with respect to one reference pdb. I have to use Align > all this to *Ca in Pymol. However, how could i do this via scripting in Pymol? As I have multiple sets of pdb files with their own reference pdb files. Is it possible to do the same in Python via Jupyter Notebook in Pymol?

I was using fragbuilder module in python to generate peptides of sizes 4, 6, and 10. However, the issue with fragbuilder module is that some of the bond angles are deviating from the standard values. For instance, C_alpha--C--N bond angle standard value is 121 degrees but fragbuilder assigns 111 degrees. This angle deviation causes a deviation in the distance between the nearest neighbor C_alpha---C_alpha and its value is 3.721 angstrom and the typical standard value is 3.8 A. Also another bond angle is a deviation from the standard value by 6 degrees which is the C_alpha---C---N whose value is 111.4 degrees and typical standard values are 117 degrees. My doubt is how much deviation is allowed for MD simulations of peptides (or proteins) while fixing the bond lengths and bonds angles ?

Recently I am stuggling to improve the kinetics of an artifical enzyme. I expressed this enzyme in E.coli and then test it's kinetics properties.

I noticed that if I pick single conies for testing, there will have a variation in both reaction rate and maxium reaction. indicating in fig.1 (the y axis represent the product that have been formed and the x axis represent the time in seconds.) 4 different conies have been picked and they all contain the same plasmid that transfection at the same time and same procedures. However there is huge differeces in the reaction rate and maxium reaction.

Then I wonder if it's due to the different conies would fold the protein differently, so I did another test by add multiple conies (actually all conies on one dish) into my culture medium. And then I test this mixed enzyme with different substrate concentration to test the affinity and kinetics at the same time. fig.2 (different color represent different concentration; the dash line represent a Imaginary limitation)

The problem that makes me wonder is that: what might be the reason for this reaction have a rate limitation?

I have few hypothesis about this phenomeon:

1. based on the Imaginary rate limitation; there might have steric effects preventing the binding of the substrate. (but I don't have see enough enzymatic reaction curve that have steric effects)

2. based on the varation between conies; this artifical enzyme might have many different ways of folding (I mean this enzyme would have many different prefered structures in different bacteria cells). maybe bactria from the same coniey would prefere similar stucture? and some stucture have better enzymatic performance, others do not.

I am really appreaciarte your reading and would be very happy to receive any response.

I want to do DNA-Protein docking at specific active site. So please help me which tool and server can i use for this type of docking.

There are so many softwares for docking but which one is best? On which we have to rely?

I have solubilized my protein with 0.3% sarcosine and purified by using Ni-NTA,during purification most protein is going into flow through.

I have diluted my sonicated sample to 0.1% sarcosine but still I am unable to get binding of protein.

Dear community.

I'm just studying for a master’s degree in the department of biochemical science & technology, at National Taiwan University.

When I try to refine the structure at Coot or search the paper about the protein structure or membrane protein.

I'm curious about what is the meaning of Fo and Fc, and the difference between the Fo-Fc map and the 2Fo-Fc map their meaning.

Why they are important when we try to fit the residues or molecules in electron density maps?

Also, I what to know does it has any program or application that can create the density map in this journal article.

The supplementary figure 6 in Astashkin, R., Kovalev, K., Bukhdruker, S. et al.Structural insights into light-driven anion pumping in cyanobacteria. Nat Commun 13, 6460 (2022). https://doi.org/10.1038/s41467-022-34019-9

It's my first time asking the question on this website and I’m not an English native speaker, sorry if I offended you.

Cordially,

Guan-Yi.

I had developed a homology modeled protein and identified the cavity of the protein through bioinformatic software. unfortunately, i couldn't calculate the cavity volume in my modeled protein. I want to get some information about the cavity volume and size in modeled protein for de novo drug design. kindly let me know the way to calculate the cavity volume of the homology modeled protein

I want to visualise secondary structures of multiple proteins aligned (something similar to this figure). Any recommendations?

Thanks in advance

Why would AlphaFold give a protein model that contains homoserine instead of serine? Is there anything wrong with the predicted structural models? Thank you.

Can the differently coloured region around the ligand be saved so that I can directly see the coloured region the next time I open it? If so, what format would be the file? pdb format? Thank you.

I used AlphaFold to predict the structure of a protein that has not been well studied.

I have a pdb file of the predicted structure.

Now I would like to identify the domains of the protein using this pdb file.

Is there a suitable tool for my purpose?

Hii, Is there a way I can extract the alternative spliced protein isoform structures from PDB? Also can we mapped the structure to uniprot sequence So we can know which structure belong to which isoform sequence?

Is AlphaFold accurate enough when the protein shares less than sequence similarity with the closest, structurally solved homologue?

Besides, how accurate is Alphafold in de novo structure prediction of protein families without solved structures?

Hi. Is it always invalid to get the docking result obtained using structures that have not undergone energy minimisation? What would be the factors considered in this decision?

YASARA Structure allows the users to build the missing residues in protein crystal structures using BuildLoop and OptimiseLoop command. If the missing residues are modelled using BuildLoop and OptimiseLoop command only without energy minimisation, is the subsequent docking result valuable and valid. In other word, should the data generated this way should be discarded as invalid?

Alternatively, is it meaningful to retain the docking results generated using the same modelled structures with and without energy minimisation, and hypothesise that the best-ranked peptides obtained in both methods can be one of the best peptide inhibitors, which can only be confirmed experimentally?

Thank you.

I want to perform targeted molecular docking of:

(a) a receptor (enzyme) whose structure is not availabe, and hence has been built by computational ab intio methods (and not homology, since the % identity is very low);

(b) a substrate whose structure is availabe.

Given that, the active sites of the enzyme are also not truly available, but has been obtained from (a) literature review; or

(b) inferred from cavities/clefts predicted by CASTp results, how exactly should I perform targeted molecular docking?

Hi. I am currently designing peptide ligands.

I noticed that DUD-E (Directory of Useful Decoys, Enhanced) can be used to generate decoys for small molecules. I wonder if DUD-E is equally useful in generating decoys for the peptide ligand.

Is there other way of decoy generation for peptides?

Thank you.

Sincerely yours,

Thai Leong

Dear all, Hope you all doing well.

I was worried about the prediction of protein-protein interaction using online servers like ClusPRO. Actually recently we found that Protein A interact with Protein B using yeast two hybrid method. Protein B exist as a complex with Protein C, D, and E. Now, biochemically, Protein A didn't show interaction with Protein C, D and E. However, when I performed the protein-protein docking using ClusPRO, it shows interaction of Protein A with all Protein C, D and E. The question is how to rely on such online servers. Because it is giving interaction with whatever protein (as receptor and ligand) you feed to the Job server. It doesn't make any sense to me. How one can differentiate in-silico that Protein A and Protein B is the better interaction propensity than other member of the complex. I cannot do Molecular Dynamics simulation for such huge complexes with all permutation and combinations, because have no expertise in it and also it will be computationally very expensive. Please explain and give your valuable suggestions this in a simple manner.

Let's say we docked Protein X with Ligand A, Ligand B and Ligand C respectively.

Meanwhile, we have three different desktops, i.e. Desktops 1-3 for molecular dynamic (MD) simulation. Can we make use of the desktops using the following way in speed up the process of getting the results from MD simulation?

First round of MD simulation:

Desktop 1 - Protein X-Ligand 1 complex

Desktop 2 - Protein X-Ligand 2 complex

Desktop 3 - Protein X-Ligand 3 complex

Second round of MD simulation:

Desktop 1 - Protein X-Ligand 3 complex

Desktop 2 - Protein X-Ligand 1 complex

Desktop 3 - Protein X-Ligand 2 complex

Third round of MD simulation:

Desktop 1 - Protein X-Ligand 2 complex

Desktop 2 - Protein X-Ligand 3 complex

Desktop 3 - Protein X-Ligand 1 complex

Thank you.

Hi,

I have been trying to minimize a protein showing invalid bond type in some residues. while minimizing it throw an error "restrained minimization has failed". please help

thanks in advance.

I generated the predicted structure of a dimer of proteins using AlphaFold2, but it has overlapped amino acids like the picture.

(PDB file: https://drive.google.com/file/d/1frFw6gH1rqvtZfVmubVm-thQ2lvli1lZ/view?usp=sharing )

Because of this, SMOG ( https://smog-server.org/cgi-bin/GenTopGro.pl ) returns an error `FATAL ERROR: Contact between atoms 356 451 below threshold distance with value 0.192` when using this PDB as an input.

What I came up with was performing energy minimization on the entire protein by MD simulation software like Gromacs or resolving a part of the amino acid sequence using molecular viewers or modeling software like Pymol.

Which is a better way or is there another way to solve this issue?

If MD simulations converges to Boltzmann distributions ρ∼exp(−βϵ) after sufficiently long time why do we need MD simulations, as all the macroscopic quantities can be computed from the Boltzmann distribution itself. This question I am asking for short peptides of sequences of few amino acids.(tripeptide, tetrapeptide etc).

For instance in the given above (link) paper, they are using MD to generate Ramachandran distributions of conformations of pentapeptide at a constant temperature. So this should obey statistical mechanics. If it is so, then this should satisfy Boltzman distributions.So I should be able to write down the distributions using boltzmann weight as follows,

ρ({ϕi,ψi})∼exp(−βV({ϕi,ψi}))

.Here, all set of Ramachandran angle coordinates of the pentapeptides is given by {ϕi,ψi}{ϕi,ψi}.

Why should I run MD to get the same distributions?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands!

what I need is to connect them into one to run molecular dynamics simulation, what is the best tool to do so, also what are the steps to make sure that it will be mostly accurate?

Hello all

Is there any reliable and free web server that runs molecular dynamics simulation of proteins?

In the PubChem database I could find a 2D structure of the compound (CID 24763) but wants a 3D structure for docking, moreover the compound is too long so is there any technique to cut it short since the compound is starch like polysaccharide??

I am trying to estimate the width of DNA from its crystal structure.

I've used phyre2 to model the protein for the simulation using Gromacs, but later I found that 2/3 proportion of the structure ( except for IDR ) had been already determined by X-ray crystallography.

The known structure contains Zn2+ to stabilize the structure of the entire protein, so I doubt phyre2 can predict decent structure. How should I model the structure of proteins using a known structure as a part of it?

Dear community,

As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data.

However, in many cases (e.g. attached image), when you visualize the densities, there are negative (red) density blobs not containing any atoms inside. Just empty space inside. There is nothing in the model in those regions of space. How it should be interpreted?

Could you tell me please what I am missing?

Would be grateful for any help,

Best wishes,

Aliaksei

I have used modeller to generate a pdb file. i have run it on PROCHECK. but the input format is not compatible. (brook haven format). How do i convert my file? or any other way? Please help. ASAP

While am running the EM, the minimizatin gets stopped before the forces get converged at step 14

Steepest Descents:

Tolerance (Fmax) = 1.00000e+03

Number of steps = 50000

Step= 14, Dmax= 1.2e-06 nm, Epot= 1.84916e+18 Fmax= inf, atom= 7809

Energy minimization has stopped, but the forces havenot converged to the

requested precision Fmax < 1000 (whichmay not be possible for your system).

It stoppedbecause the algorithm tried to make a new step whose sizewas too

small, or there was no change in the energy sincelast step. Either way, we

regard the minimization asconverged to within the available machine

precision,given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, butthis is often not

needed for preparing to run moleculardynamics.

You might need to increase your constraint accuracy, or turn

off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.9#

Steepest Descents converged to machine precision in 15 steps,

but did not reach the requested Fmax < 1000.

Potential Energy = 1.8491607e+18

Maximum force = inf on atom 7809

Norm of force = inf

What should I do?

A number of post translational modifications can occur to a protein, including phosphorylation, methylation etc. I am aware that there are a number of servers and tools to predict positions for these modifications based on sequence and/or structural patterns or motifs. However, is there a tool (or server) available that can actually model them on a structure (or a model)?

Given:

1. The nearest neighbor of 𝑝𝑖 then 𝑝𝑖-𝑝𝑗 is a Delaunay edge.

2. In a 3D set of points, if we know that consecutive points ie... 𝑝𝑖-𝑝i+1 are nearest neighbors.

3. The 3D points do not form a straight line

Assumption:

Each Delaunay tesselation (3D) has at least 2 nearest neighbor edges.

Is my assumption true? If not can you please explain to me the possible exceptions?

Thanks,

Pranav

I would like draw protein 3-D structure? Can anyone suggest me the best software that I can buy?

Hi everyone,

I need to do MD simulation of wild type and ten variants at 50 ns. I am looking for a low-cost cloud service/ simulation environment. Would you please suggest me any?

Thanks in advance.

I had used SUMMA server for structure refinement.

Hi,

Typically, the solvent accessibility of water-soluble protein is computed by using a water molecule with a size of 1.4 Å). For my research work, I need to compute the relative lipid (-CH2 as a probe molecule) accessibility for membrane protein structures through NACCESS program. In this regard, I don't know how to change the solvent parameters in NACCESS.

Is there anyone who can help me with this calculation?

Thank you in advance.

Hello everybody! Somebody knows an open source software for induced-fit docking? I have to dock ligands on receptor-models which have low sequence identity with the template (13-20%) and I was thinking that an induced fit docking can help me to improve the quality of my models, at least in the binding site.

I want to run protein-Ligand simulation where gold atoms are ligand. Gromacs is showing error for that. I tried to use Prodrug server also, but it is not generating coordinates for gold atoms. 

Can anyone help me in this?

I want to compare the active sites of some protein models in quantitative way (their volume or dimensions), Is this option available in the following softwares (MOE, YASARA, Pymol, Chimera) as I have access to them only. If any one had a similar experience with one of these softwares specifically.

Dear all,

I am a beginner and I have plotted dssp plot using cpptraj for the first time using following script;

> dssp.in

trajin md-sim.ncsecstruct 1-263 out dssp.gnu sumout dssp.sum.agr

I wanted to know that what is None in dssp.gnu plot. I have read in amber manual that None is nothing just 0 integer. If it is correct so why cpptraj secstruct script plot None. Can I exclude this from dssp plot. Kindly help me.

[set cbtics {"None", "Para", "Anti", "3-10", "Alpha", "Pi", "Turn", "Bend"} ]

Thanks.

Ignoring a proteins sequence, say I have a predicted contact map plotted from a useful tool like ConKit, it can be quite easy to determine general regions of secondary structural features and if is running paralell or anti-paralell etc etc..

However besides this, does anybody have any good tips for breaking the predicted contact map down further to see regions which could be contacts involving loops or helices-loop contacts? In essence I am seeking some tips for how someone would step-by-step analyse different factors from a predicted contact map.

I have been analyzing 90-amino-acid fragment of a protein using HSQC and triple-resonance (¹H-¹⁵N-¹³C) NMR. I know roughly where arginine, lysine, and tryptophan side-chain peaks lie on the HSQC, but how can I definitely distinguish what is a backbone and what is a side-chain? In addition to the HSQC, I have several 3D experiments (e.g. CBCANH and CACB(CO)NH).

in many insect including Lepidoptera, there are two kind of sperm: Eupyrene and Apyrene. how can we distinguish two kind of sperm in pictures?

I need to find weather a region of a protein that I'm currently working on has a Calcium Binding Domain. The putative region has a similar amino acid profile as an EF domain.

I would like to run the sequence through a tool and get some proper perdition results 

I saw on many journal articles, showing the predicted EF hand domains with  EF hand test results. (Attached image)

Can anyone please suggest me a proper prediction server that I can use :)

Thank You

what is the best protein design program that can assess the effect of mutation in a globular protein structure? i am looking to change the specificity of a protein. but mostly i am interested to measure the outcomes of the mutation on the protein itself rather than the interaction. and if i want to look into the interaction as well should i use protein design or MD softwares?  

3d structure of a protein is made up several secondary structure elements like helices and sheets. How to find the number of these elements in a pdb file?

Can't access CastP(an online tool for surface analysis of protein) from links i've found through google(http://cast.engr.uic.edu/castp/calculation.php, http://sts.bioengr.uic.edu/castp/)

I guess their server is down or i'm trying the wrong URL. Please suggest me any alternative.

I would like to understand the reason why proteins show frothing.

I'm currently trying to get the 3D structure of a set of peptides (ranging from 12 to 20 aminoacids). Subsequently we want to make docking analysis against an enzyme.

Which software do you use for that? How do you refine the structure?

Thanks!

Hello structural biologists! I am interested in developing an inhibitor to target the assembly of a specific heteromultimeric complex. The complex exists in the cytoplasm of most eukaryotic cells. A crystal structure of the entire complex is available. I am interested in targeting the interaction surface between the two proteins.

The binding surface is comprised of two alpha helices, one from each protein. I am aware that PPIs are considered a particularly tough target for inhibitor development. However, I have an advantage here, as several residues in close proximity are known to be essential for complex formation. In a sense, these residues seem to form a binding pocket, albeit one shared between two proteins.

My goal is to develop a pharmacophore model of this 'binding site' so that I can apply virtual screening to look for compounds that can mask this interaction. I have not found much information on the generation of multi-protein pharmacophores. I would be grateful if someone could point me in the right direction.

Regards,

Patrick

I'm interested about a monoclonal antibody Rituximab, I've found pdb structure of Fc and Fab regions of this. Is there any too/method that I can use to append these and get the full pdb structure?

Fc fragment: 1L6X

Fab fragment: 2OSL

I need a software to draw chemical structures. I have been using the free trial version of ChemDraw, which has expired.  Now I am looking for an alternate software that can do chemical drawing. I am not looking for any special or advanced features. I just need a software that can  generate good quality images for use in publications? 

Simulation has been extended till 70 ns, but still there is no sign for my protein to become stable. What could be the reason?

My protein is a monomer with two helices connected with a middle linker region of 3 amino acids.

Kindly throw some light.

input: amino acid sequence

output: potential protein binding partners to sequence

Thanks for taking the time to address my question.

Bre

I have about 2000 of proteins ligands from Protein Data Bank and a lot of their characteristics like full name, molecular formula, SMILES, etc. I would like to classify them in several broad groups according to their chemical features. Is there any database with such data?

Thank you!

How should I rename the ‘Zn’ as ‘M’ and provide energy coefficients for Zn in Autodock Tools? I have just started with autodock tools. My protein has Zn ion in it. In the tutorial, it says something about Grid macromolecules.

"ADT also determines the types of atoms in the

macromolecule. AutoDock can accommodate up to 7 atom

types in the macromolecule. It uses a standard set with two

customizable types, ‘X’ and ‘M’. If your macromolecule has a

non-standard atom type, ADT will prompt you to set up a

customizable type X or M for it by entering energy parameters.

For example, Zn is not in the standard set. If your

macromolecule has Zn, for AutoDock you have to rename the

‘Zn’ as ‘M’ and provide energy coefficients for Zn. ‘X’ can

be used as a second customizable type. It is not possible to

have more than 7 types in the macromolecule."

I do not know how to rename and give charge to Zn. Every time I try to save the file as .pdbqt, it gives 0.000 to Zn. [WARNING: These atoms have zero charge: Zn].

I tried using a PDB file editor, but I always do something wrong.

If someone could help in this aspect.

Thank you very much in advance.

We are trying to join a dsRNA with a peptide using HyperChem. The moment we are trying to invoke the model builder, the double stranded structure just mashes up in a weird mesh like thing. Whenever we are trying to optimize the geometry using steepest descent or conjugate gradient or Newton-Raphson, a lot of Oxygen appears from nowhere (which do not show up in other visualization tools like PyMol or VMD). And when we are trying to join the peptide without doing the geometry optimization (the most unscientific thing I have ever heard of), the connecting bond just becomes a long stretch of line (which it should not be, because there's a permissible limit of bond length, isn't it???)

Can anybody shed any light on how to do this job in HyperChem??? We are open to other softwares also, if required.

I have a list of protein pairs that interact with each other, which was obtained using yeast-two-hybrid.No 3D-structure or other deeper structural information.

My tutor wants me to find out the protein-protein interaction site of these pairs using some bioinformatic tools.

I know nothing about bioinformatics or structures,so is this possible to do? can anyone recommend some good programs that can predict PPI sites?

Dear researcher,

I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an error.

"Atom SE46 in residue CYS 597 was not found in rtp entry CYS with 11 atoms while sorting atoms"

please give me any suggestion how i can add the selenium during MDS.

Hi,

We are trying to draw a charged amine structure in HyperChem. We jotted down the structure as usual but it is showing without any charge.

Anybody has any idea about how it can be done???

I have been reading that it is important for decoys (inactive molecules) to have similar physico-chemical properties to their matching ligands but different topology in virtual screening benchmark data sets

Why is it that? Does topology play a big role in discriminating ligands from decoys? 

What is the role for topolgy in protein-ligand interaction? 

Would you mind giving me a hint or recommend me some material that I could read? 

Thank you so much for all the help that can be provided :)

Hugs,

Stellamaris

I isolated my protein complex from mammalian cells. Purify it using affinity purification methods. but after running chromatography the concentration became very low to go further structural study. How can I I increase concentration without affecting the protein complex? 

MODELLER website's  "difficult tutorial", available at link below, makes mention and use of "mGenThreader" software. Problem is: provided website by tutorial where mGenThreaded should be doesn't has the option to use mGenThreader, neither I've found any website for which I can download it. Instead of it, I've found "GenThreader" and "pGenThreader".

So I ask: Where Can I download mGenThreader? If this is not possible, may I use pGenThreader in place of mGenThreader?

Dear researcher,

                           I want to dock a small protein in the interface of diamer protein. When i submit the diamer structure in to HADDDOCK server it terminates the jobs and do not produce the result. But when i delete the one chain of diamer and proceed the docking it accept and produce the result.

So question is:

is there any problem in diamer construction. If yes please suggest me how to create the diamer.

is there any problem in docking then how can i resolve it.

I am trying to calculate SASA scoring function using dock 6.7. However, I am confused about the interpretation of the score.

I have obtained:

SA_Descriptor Score: 14.15

How could I interpret it? What do highest  scores mean? What do slowest scores mean?

I would really appreciate all the help that can be provided!

I have a protein which has two chains each contains 422 residues, both chains are identical. I want to model this protein but the target sequence which I have contains more than 850 residues. When I combined the two chain residues as a single chain and aligned them with the target sequence it got aligned with the whole 850 residues target sequence and showed 56% identity. I want to model this two chains template protein into a single chain using my target sequence. How can i do it? Any suggestions?.

Is there a way to choose the site where we want to place the grid box using the command line?

When creating the grid parameter file in ADT, in the graphical interface, you go to Grid ---> Grid Box --> Center. Then you have to chose to center the grid box in either: 1) Pick an atom 2) Center on ligand 3) Center on macromolecule 4) On a named atom. Therefore, it is possible to chose to center the grid box in the ligand.

My question is how can you do it (chose the position of the grid box) with the command line? Is there a script that I could use? There is no option in the grid parameter file. I have more than 10000 compounds and it would take me a really big amount of time to do it graphically. Then, I would like to automatate the process. Is there a way that I can do it?

I am going to do rescoring which means that the grid will not be in the same place of the ligand automatically.

I've isolated a new drug and would like to see the effect on the murine of S. aureus using Autodock

For example, it is known that one protein is destroyed in ubiquitin-proteasome system, but the E3 ubiquitin-ligase that performes ubiqutilation of this protein is unknown. How can I predict which E3-ligase ubiqutilates this protein? I can find aminoacid sequence of the protein, I know sites for ubiqutilation in this sequence, I can find also information about secondary and tertiary structure of the protein.

Hi all,

I am learning a lot of things about the computational biology for the first time. I was curious, with the current technology, what is  the possible simulation time range for a research in computational biology using commercial force fields such as AMBER, GROMACS, CHARMM etc? Can we go more than ns without harming the results? 

Thanks!

I am doing some researches about the 3D structure and binding site of DHFR, I wanted to have any 3D model for BH2 binding with DHFR. I could just find some models for TH2, but not for BH2.

Could some one provide me any model, or paper where I can find such modeling? it is not bad if there were any clear modeling for TH2 as well.

Thanks in advance!

Hi!

I was wondering if you can suggest program/script for linux or not, that can calculate the interactions between Ligand and protein from a pdb file. When I'm saying interactions i mean, h-bonds, aromatic interactions, hydrophobic bonds etc.

I found IChem on the internet, but it seems that it doesn't work properly. I couldn't even run it.

Thanks

Dear CHARMMers,

can anyone tell me what's the issue?

I try to run calculations with charmm for homology protein file, and when it comes to reading psf file (generated with par_app36_prot.prm file), the error occurs:

"Atom 1 0 NH3 problem in psf

***** LEVEL -3 WARNING FROM <psf_read_formatted> *****

***** atom type not found for atom"

Anyone might help to handle it?

Kind regards