57
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DeepMind just announced a breakthrough in protein folding, what are the consequences?
Imagine if given an amino acid sequence, you could quickly calculate what the shape of the corresponding protein would be.
You would be able to predict what effect a mutation would have on the shape ...
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18
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Introduction to protein folding for mathematicians
Great question! Protein folding has been in open question for decades. Just recently, there's been a lot of discussion regarding DeepMind's AlphaFold project, which was discussed at length on our very ...
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Does DeepMind's new protein folding software (AlphaFold) also work well for metalloproteins (proteins with metal cofactors)?
It's a great question! Some of my answer will be taken from my answer to your question on the AI stack exchange, but cross-site questions are allowed and your question here is slightly different so my ...
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14
votes
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How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?
The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here:
The main issue are the units. The input parameters for reax force fields ...
- 1,401
14
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How to calculate the computational time required for a MD simulation
The simulation speed and efficiency depends on the hardware and software that you use. Things that you should keep in mind are,
Every computer is unique in its ability. So only someone with access to ...
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12
votes
Introduction to protein folding for mathematicians
Someone more familiar with the problem might have a better suggestion, but I recently came across Daniel B. Dix' notes on Mathematical Models of Protein Folding. This is not my field, so I won't ...
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11
votes
What are the factors to consider before docking 2 proteins?
The main requirement is to have structures files with good resolution. According to RSCB PDB documentation:
Resolution is a measure of the quality of the data that has been collected on the crystal ...
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11
votes
How to calculate the computational time required for a MD simulation
Short answer: Do a short test run for performance estimates. Once you're familiar with a specific hardware/software combination, you may be able to estimate based on the size of the system, but the ...
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10
votes
Introduction to protein folding for mathematicians
Preamble
Since I don't know your specific background, this is a generic answer for any applied mathematician wishing to enter the field of protein folding. Not everything will apply specifically to ...
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9
votes
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What is the procedure to develop a new force field for molecular simulation?
The most useful answer to "how do I develop a novel force field for proteins" is "don't". (Or collaborate with a group which does.)
Developing a protein force field is ...
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8
votes
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Chimera or other software to perform protonation states of a protein
H++
H++ is a web service that permits to protonate your macromolecules using using different pH conditions.
From its site:
H++ is an automated system that computes pK values of ionizable groups
in ...
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8
votes
Which non-commercial software can be used to dock two proteins?
HADDOCK
HADDOCK is both a web service and a standalone code.
From the web server:
HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the ...
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8
votes
Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?
Yes, it is possible. Of course, the original residue numbering will be lost; but you can certainly recover the sequence, and number the residues within any contiguous chain.
How to do it really ...
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Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?
Statistical mechanics: is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities [this is the first line in the linked article].
...
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7
votes
DeepMind just announced a breakthrough in protein folding, what are the consequences?
Keep in mind that many if not most proteins have multiple quasi-stable conformations, so their 3D structure is not actually a single conformation but rather a Markov matrix of conformations, with ...
- 71
7
votes
DeepMind just announced a breakthrough in protein folding, what are the consequences?
Probably one of the important applications is Computer Aided Drug Discovery (CADD). If the protein structure could be accurately predicted, one could design protein-ligand docking on the binding ...
- 3,813
7
votes
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Dihedral angles of alanine dipeptide
Proteopedia suggests that the $\phi$ and $\psi$ angles of a Ramachandran plot only involve carbon and nitrogen atoms in their definition and specifically the carbons and nitrogens in the backbone of ...
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7
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Alternative to CGenFF for generating large ligand topology
I'd use OpenMM's openmmforcefields package, which is available on GitHub.
I haven't used it extensively, but I recommended to a student in a colleague's lab and ...
- 9,045
7
votes
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Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides
I'm not sure if it's improper to answer my own question, but I think I've cracked it.
For each peptide bond match identified by GetSubstructMatches the index [1] is ...
- 121
6
votes
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Finding conformations of peptide based on dihedral angles
I don't think that any classification of dihedral angles exists.
α and β that you see in the picture refer to alpha helices and beta sheets – structural elements of proteins (secondary structure).
...
- 1,780
6
votes
How much of a difference in a protein's radius of gyration can be considered significant?
It depends on your actual scenario. If we assume that you have two Molecular Dynamics (MD) replicas for the same protein (and their respective trajectories), then when you perform a Radius of Gyration ...
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6
votes
How to characterize surface features in proteins?
Normally, if various proteins have the "same" cavities/clefts, this means that they are part of the same family and the amino acids that form the cavity are conserved.
I really don't think ...
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6
votes
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Calculating RMSF in VMD
The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely ...
- 453
6
votes
Protein structure prediction
I'm adding another answer because I recently find these news. The machine learning-based methods alphafold and rosettafold were recently released on github. Someone has just implemented it in Google ...
- 1,479
6
votes
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Protein structure prediction
Here's what I did. Assuming that you have a part of the protein crystal structure.
In my case, I have an incomplete structure of the protein. Lets say if I have an amino acid (AA) sequence of 520 (...
- 1,291
6
votes
Secondary structure information at each frame in a VMD trajectory
I have found the solution to the problem. One needs to use the animate command to change the frame in the top molecule in VMD. The corrected script which produces ...
- 453
6
votes
How to extract specific frames/model from a multi model pdb file?
Do you have access to OpenBabel to run from the terminal?
For the purpose of demonstration, the example following is demonstrated on a file listing SMILES strings. However, the concept may be applied ...
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6
votes
Accepted
How are diffusion coefficients calculated?
There are several different methods to calculate diffusion coefficients depending on the problem and some nuances to consider.
Mean square displacement
The most common way to calculate diffusion ...
- 1,901
6
votes
Does Bioinformatics have any relationship with protein modeling and simulation?
Yes - protein and RNA folding has been a subject of research in bioinformatics for several decades, and have received much development in the last couple of years due to application of machine ...
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What does it mean by a "restraint" in the case of a protein chain?
They go on to describe exactly what they mean by a "restraint" later in the paper in the section "Materials and Methods::Cα and side chain centroid restraints".
A Cα atom at ...
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