Questions tagged [proteins]

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Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
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Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...
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How do I validate a new monte carlo scheme? [closed]

Suppose I design a novel variant of the Monte Carlo algorithm for polymer simulation. How can I test the validity of my novel algorithm?
user366312's user avatar
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How do I validate and benchmark a new protein or polymer model?

Suppose I designed a novel coarse-grained model of polymer chains. How can I test the validity of my novel model? Is there any applied framework available?
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?

Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
Don Aborah's user avatar
2 votes
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Method for Energy Computation of Protein Structures

So far i have found only one paper that describes how we can compute protein energy while doing MD simulation: Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
user366312's user avatar
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3 answers
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Which MD software is preferable for protein simulation?

I see that some free MD simulation software are available online. VMD NAMD LAMMPS OpenMM GROMACS Amber CHARMM Which one above is the most appropriate for protein simulation?
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From a PDB file, how may I know which atoms have bonds between them?

Suppose I have a protein PDB file, and I want to know which atoms have bonds between them. How can this be done? Sometimes people suggest using the CONECT field for ...
user366312's user avatar
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How easy is it to distinguish water from ions in xray crystallography?

I'm interested in bound ions in protein xray crystal structures. Of course a lot of structures include biologically significant ions, such as Mg2+ in the active site of an enzyme. But a lot of ...
Alex I's user avatar
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How to select charge and multiplicity for macro-molecules?

In optimising proteins with DFT/B3LYP, how can we detect the charge and multiplicity of the protein?
PriZarah's user avatar
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How to find the smallest distance between 2 residues in Pymol?

I am very new to Pymol and was trying to figure out how I can find the largest distance between 2 residues. Using just the basic distance function I get multiple distances which is not very useful in ...
Faheem Azeemi's user avatar
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What is the procedure to develop a new force field for molecular simulation?

Suppose, I want to develop a novel force field for proteins. What is the empirical procedure I should follow to do that?
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Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?

I am looking for relevant books to study the modeling and Monte Carlo simulation of protein chains. I see that books related to Statistical Physics, Statistical Mechanics, and Molecular Modeling have ...
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Can you supply me with some book names on MC protein simulation?

Is there any book written on protein simulation specifically using the Monte Carlo technique (i.e., not QM or MD)? If so, can you supply me with some names of such books?
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What does it mean by a "restraint" in the case of a protein chain?

Discrete restraint-based protein modeling and the Cα-trace problem We present a novel de novo method to generate protein models from sparse, discretized restraints on the conformation of the main ...
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Does Bioinformatics have any relationship with protein modeling and simulation?

Does Bioinformatics have any relationship with protein modeling and simulation? In other words, is there a research area where Bioinformatics uses protein modeling and simulation to achieve its goal ...
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Computationally predicting small molecule/peptide based on others' binding to target protein [closed]

Say you have a small molecule or peptide that binds to a protein of interest. I'm interested in predicting the properties of the other type of ligand that might bind in a similar way. For example: A) ...
weddegege's user avatar
4 votes
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Force field for charged peptide-ion system

I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
Arete's user avatar
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How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?

I asked this at Biostars but the post seems to have been deleted there. My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
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3 votes
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Why is the Alphafold PAE (predicted aligned error) not symmetric?

Cross-posted on AI Stack Exchange. We are running alphafold2 multimer on Google Colab to predict the association between two proteins. It generally works fine, but we get an asymmetric PAE plot for a ...
NKGon's user avatar
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Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?

Let suppose that, for a given reason, a PDB file (with all the residues/chains/heteratom/cofactor/ligand information inside) is converted to a XYZ file. Doing that, all protein information is lost. ...
Camps's user avatar
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How can I compute the performance of an application software? [closed]

I am working with protein PDB files. Application 'A' generated 3884 PDB files from the protein's CA-trace. Application 'B' did the same. So, I calculated the CRMSD values of each pair of files for ...
user366312's user avatar
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Why do I see a deviation when I compare PDBs using TMalign?

I constructed a PDB file of main-chain from its CA-trace using pd2_ca2main app. I used TMalign to compute RMSD values from those ...
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Why is this source code giving incorrect RMSD value?

Aligning PDB structures with Biopython The following source code is obtained from the above link: ...
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Why do we need to find minimum energy in a protein chain?

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models The above research paper is about a software tool for reconstructing a protein's main chain model only ...
user366312's user avatar
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3 votes
1 answer
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Perform energy minimization of multiple models of protein-dna complexes

Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)? I know of GROMACS or Chimera or the online servers but is ...
Lily Sharpton's user avatar
7 votes
0 answers
167 views

How to make an idealized infinite alpha helix or beta sheet?

I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
Alex I's user avatar
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3 votes
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390 views

How to fix outliers in Ramachandran plot using Coot [closed]

I have the following Ramachandran plot generated by Coot: Notice that it has high outliers content (red dots). I want to manually drag those red dots into some part of the region. Eventually, I ...
littleworth's user avatar
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5 votes
0 answers
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Simulated annealing of small protein [closed]

I understand the general concept of simulated annealing and have seen various criteria in papers, but I was wondering if there is a general rule of thumb for selecting a final structure, how many ...
Ga3258's user avatar
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1 vote
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What does "dynamics" mean in matter modeling?

As an example, I have seen the phrase "dynamics of proteins" or "dynamics of biomolecules". The review paper "Protein Dynamics" by J A McCammon has the word in its title, ...
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2 votes
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How can I calculate the radius of a residue? [closed]

I want to read a PDB file and display/render the atoms using a graphics engine. If I consider each residue in the protein file as a solid sphere, what would be the radius of the sphere? How can I ...
user366312's user avatar
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6 votes
2 answers
2k views

How to show orientation axis in Pymol

Is there a way to show the orientation axis in Pymol? It's something like this in VMD. I much prefer Pymol rendering.
littleworth's user avatar
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6 votes
2 answers
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How are diffusion coefficients calculated?

To support my laboratory result, I'm searching for an MD/statistical mechanics approach to predict translational diffusion coefficients in the liquid phase. I'm aiming to describe small peptides and ...
Giuseppe Basile's user avatar
2 votes
0 answers
47 views

Can protein modeling and simulation be used in developing a marketable product? [closed]

As we all know computer science, electrical engineering, etc. knowledge can be used in developing software and electronics/electrical products that can be sold to end-users (B2C). Can protein modeling ...
user366312's user avatar
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4 votes
1 answer
203 views

What is the curve fitting model used for the "Qubit™ Protein Assay Kit"?

This is the example of Qubit™ Protein Assay curve. It relates the concentration (x-axis) with fluorescence (y-axis). What is the curve-fitting method it use for this? Clearly this is not simple linear ...
littleworth's user avatar
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2 votes
1 answer
104 views

What do we simulate with molecular simulation of proteins in the theoretical research?

I know that the following can be simulated: secondary/tertiary structure prediction protein-surface/protein-protein interaction tests protein-ligand binding test I wonder if references or ...
user366312's user avatar
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3 votes
1 answer
441 views

Domain decomposition error while applying bonded restraints - GROMACS

GROMACS version:version 2021.3-MODIFIED GROMACS modification: Yes Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
Vasista's user avatar
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4 votes
0 answers
45 views

How reliable is Alphafold 2 for folding random-coil peptide [closed]

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
neversaint's user avatar
5 votes
1 answer
302 views

Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides

This is a variation of a question asked on October 30, 2021 here, but it is different enough that I think it warrants a new post. I'm also trying to use RDKit. Is it possible to convert a SMILES ...
CCranney's user avatar
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5 votes
1 answer
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Why are ligands restrained when simulating a protein-ligand complex with MD?

Currently I'm doing an MD simulation of a protein-ligand complex using GROMACS. In the tutorial it mentioned the process of Restraining the Ligand. Why do we do it? Is it absolutely necessary?
littleworth's user avatar
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8 votes
1 answer
547 views

Alternative to CGenFF for generating large ligand topology

I am now preparing a ligand topology following GROMACS protein-ligand tutorial. However, I have a large ligand (446 atoms). $ wc -l my_ligand.pdb 446 my_ligand.pdb ...
littleworth's user avatar
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7 votes
0 answers
152 views

How to determine minimum reasonable MD timing for ligand-protein complex [closed]

I am working on protein-ligand complex MD simulation using GROMACS. Now I'm running the tutorial. ...
littleworth's user avatar
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4 votes
0 answers
67 views

A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
BND's user avatar
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10 votes
2 answers
3k views

How to calculate the computational time required for a MD simulation

I have a ligand and receptor to simulate with MD. These are my specs: Receptor has 4674 atoms, Ligand has 273 atoms CHARMM force field MD software GROMACS Computing machine: Amazon g4dn.xlarge (1 GPU ...
littleworth's user avatar
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6 votes
1 answer
3k views

How to show electrostatic interactions in Pymol or other on the wanted residue

I have the following Pymol visual, The green molecule is receptor and red/yellow is the ligand. In the ligand I highlighted Lysine (K) residue as yellow. What I want to do is to highlight and draw ...
littleworth's user avatar
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6 votes
0 answers
48 views

How to look for specific structural motifs in proteins? [closed]

Is there a way to search to search for specific structural motifs in proteins? For example can a database where we can find structures with zing finger motif or an hairpin... PDBeMotif (ebi.ac.uk) has ...
BND's user avatar
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6 votes
3 answers
465 views

How to extract specific frames/model from a multi model pdb file?

I have a multi model pdb file and would like to extract the last frame or any other frame from it.
BND's user avatar
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2 votes
0 answers
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Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
user4100's user avatar
6 votes
1 answer
91 views

How are tertiary protein structures represented in computers?

What data structure is used in representing protein structures in computers so that we can apply algorithms? Matrix or Graph or tree? P.S. I am absolutely new to Bioinformatics.
user366312's user avatar
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6 votes
1 answer
855 views

Secondary structure information at each frame in a VMD trajectory

I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list to calculate the secondary structure ...
Roni Saiba's user avatar