9 votes
Accepted

Is there are theoretical limit to the number of proteins possible and their respective structure?

You can certainly estimate a theoretical limit, given some assumptions. Let's say you do not care about any post-transcriptional modifications, you are interested only in the primary sequence. There ...
Domen's user avatar
  • 1,929
8 votes

What was the first piece of work in computational biology?

I don't believe you'll ever find the first work in bioinformatics (or computational biology, as you put it), however the field really began in the times of accumulating data about protein biochemistry....
Alina Davydov's user avatar
8 votes
Accepted

Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

The two most common families of scoring matrices are BLOSUM and PAM. Each of them has a score for every possible alignment combination between the 20 standard amino acids1. They both do more or less ...
terdon's user avatar
  • 12.8k
8 votes
Accepted

What was the first piece of work in computational biology?

Another nomination, if you include infectious disease epidemiology as part of biology and hence computational simulations of epidemics as part of computational biology: Measles periodicity and ...
Ben Bolker's user avatar
  • 5,354
5 votes
Accepted

Olympic's epidemiological impact on Zika?

Though I have not found direct access to a model (which is what I'm really looking for), I have found evidence of such modeling efforts. The CDC apparently put out a risk-assessment report in mid ...
theforestecologist's user avatar
5 votes
Accepted

What are we missing about the real workings of the evolutionary process?

The question appears interesting and made me think but I might not fully understand it. Let me know if I am answering your question. Genetic algorithm vs simulation of evolutionary processes I think ...
Remi.b's user avatar
  • 68.1k
5 votes
Accepted

Are there any sustained efforts to model existing ecosystems?

Such a model would require a fairly detailed and complete biological inventory as well as detailed knowledge of the species' interactions, and a detailed map of the physical and chemical makeup of the ...
acvill's user avatar
  • 8,286
4 votes

Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

A scoring matrix is used to compute a score for finding identical 3-letter words or similar 3-letter words that takes into account the liklihood of one being related to another. Although these ...
David's user avatar
  • 25.2k
4 votes

Examples of biological turing machines

There have been several Turing machines constructed using DNA computing. One of these machines has been used to solve the boolean satisfiability problem, another was used to solve the bounded post ...
Thawn's user avatar
  • 1,239
4 votes
Accepted

What are some useful (starter) metrics to use on phylogenetic trees?

Here are a few metrics you can calculate to get you started. You can use R to perform these calculations. Net Diversification Rate (r) Net diversification rate is (rate of speciation - rate of ...
C_Z_'s user avatar
  • 2,485
4 votes

Interesting examples of models

Biology is a large field of knowledge! As you give examples drawn from population biology (logistic population growth and Lotka-Voltera models), I will assume you are mainly interested in ecology and ...
Remi.b's user avatar
  • 68.1k
4 votes

How many atoms has the smallest known bacterium?

Let's take the example of the model bacterium E. coli, for which one can find the numbers for a wet cell of a dry mass of 0.28pg. If you have a feeling for how much smaller the smallest known ...
S Pr's user avatar
  • 6,202
4 votes

Is it possible to determine the initial population given the final one?

For the logistic equation, $$\frac{\mathrm{d}N(t)}{\mathrm{d}t} = rN(t)\left(\frac{K - N(t)}{K}\right)$$ the solution that allows you to calculate population population size at any time is: $$N(t) = \...
Chris Moore's user avatar
3 votes

Do free computer programs exist that can simulate drug permeability in bacterial membranes?

I currently work alongside many biologists that are working on simulations of anti-microbial peptides in the membrane. These seem to have a similar mechanism to what you're aiming for — ...
James's user avatar
  • 11.3k
3 votes

What was the first piece of work in computational biology?

Depending on your definition of computational biology (e.g. bioinformatics and mathematical modelling can be quite different), there is an oft-cited reference to Alan Turing's work after the second ...
Joe Healey's user avatar
  • 1,301
3 votes

A good software for agent based modelling?

My boss is a big fan of Repast HPC, but since Repast is a C++ framework it might not be the right choice for you. It takes a loooong time to write a good C++ program (even for someone who already ...
tel's user avatar
  • 3,781
3 votes

Is it possible to create a restriction map using python?

I agree with the previous answer. You can certainly write a solution in python, but have to formulate it as an algorithm first. Doing so will enable us to suggest an actual solution. Also, I wanted ...
Noushin's user avatar
  • 176
3 votes

Is it possible to create a restriction map using python?

First I'll answer this question on the assumption that you are learning or about to learn python (perhaps because you have heard it's become popular in bioinformatics) and you wish to know whether it ...
David's user avatar
  • 25.2k
3 votes
Accepted

Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?

MD is used for studying structural changes. Simulation of biochemical pathways involves the kinetics (you are not really looking at how enzyme structure changes when it binds to substrate). You can ...
WYSIWYG's user avatar
  • 35.5k
3 votes

Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

Have a look at Biopython There are specific questions about the specific internal coordinates on Bioinformatics forum i.e. : https://bioinformatics.stackexchange.com/questions/18849/help-using-...
pippo1980's user avatar
  • 131
3 votes

Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one ...
ajd's user avatar
  • 153
3 votes

Are there any sustained efforts to model existing ecosystems?

Depending on how you define "model an ecosystem" the answer is somewhere on the spectrum from "yes, it's routine" to "no, that's impossible." Let's start with the ...
jakebeal's user avatar
  • 6,977
3 votes
Accepted

Making sense of infinite-sites mutation but finite-sites recombination coalescent simulator

Caveat: never personally used ms, I might be missing a subtlety of how this model is intended to be used. I think it's useful to see how Hudson himself writes about ...
Maximilian Press's user avatar
2 votes

How many residues can a reliable ab initio structural model contain?

Year on year reliable ab initio predictions are becoming more common for longer proteins. 400 residues is not an unfeasible length. Of course, loops still remain more of a challenge than helical and ...
James's user avatar
  • 11.3k
2 votes

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

No. Methods for multiple sequence alignment (MSA) like T-coffee, which you mention, and Clustal (http://www.clustal.org), which is also widely used, employ heuristics for the alignment for the very ...
David's user avatar
  • 25.2k
2 votes

What was the first piece of work in computational biology?

I don't have any idea about the first paper in computation biology (interpreted by me as papers that use computers and computer simulations to solve biological problems). However, some population ...
fileunderwater's user avatar
2 votes
Accepted

Are neurons roughly a magnetic dipole?

Yes, neurons can be modeled as magnetic dipoles. In fact, that is the basis of MEG. Here is an example of a paper that instantiates a computational model of magnetic dipoles in order to explain MEG ...
honi's user avatar
  • 193
2 votes

How do you derive steady-state conditions from the open-state differential equation of ion channels?

These are really math problems (algebra and basic calculus) rather than biology problems. Oinf comes from solving algebraically the first equation you posted for steady state: i.e., when dO/dt = 0; ...
Bryan Krause's user avatar
  • 45.3k
2 votes
Accepted

Spatiotemporal patterns in neural networks

Unfortunately, I haven't looked at this sort of literature for a long time, but here are some thoughts with which to start. Your question is about "spatiotemporal patterns" of neural systems. One of ...
user3658307's user avatar
2 votes

Calcium concentration in activated dendritic spines?

An earlier source for an estimate of ${[Ca]_{i}}^{+2}$ in spines comes from hippocampal slices of P13-P19 rats (Majewska et al. 2000). The resting ${[Ca]_{i}}^{+2}$ in this paper was ~80 nM and a back-...
vkehayas's user avatar
  • 1,198

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