Questions tagged [protein-structure]

The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.

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DMPfold: number of models produced using “10 500” feature in “run_dmpfold.sh”?

I ran suing this command: run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 From my previous discussion, I understand that I should run ...
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13 views

Download protein structure from gene name

I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.
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From ensembl id to protein structure

Forgive me if this question is too trivial. I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this? Is there any script(python, R) so that ...
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24 views

DMPfold: Understand the run of DMPfold “run_dmpfold.sh”?

I ran dmpfold using this command: run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log It produced files like ...
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DMPfold: is it suitable to get 5000 models to compare with rosetta

I ran this command for 10 iteraions and 500 models. run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log I am ...
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Dmpfold error “No such file or directory: 'best_qdope.pdb'” when running “run_dmpfold.sh”?

I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error: ...
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I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets. I only have their protein symbols. I want to get structural data (atomic coordinate) from PDB at once, either programmatically (Python or R) or with a web ...
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25 views

DMPfold error while running protein structure prediction

I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between: ...
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PDB codes for misfolded proteins?

I'm searching for PDB code examples for "healthy proteins" and misfolded ones, so I can compare the 3D structure. I'd prefer pairs of a "protein misfolding disease", but could be any. Can I find such ...
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54 views

What is the best way to start with Structural bioinformatics with zero prior experience? [closed]

My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to ...
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Possible evaluation or validation of predicted 3D protein structure generated by SCWRL4

I mutated a wild type protein structure using Scwrl4. How can I evaluate or validate the reliability of the predicted structure generated by Scwrl4?
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Evidence of emergence of “genuine” novel protein interactions by aa mutation [closed]

Anyone knows of an example of a protein that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other ...
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Find similar proteins with similar tertiary structure?

I'm a mathematician studying knotted curves and am trying to find some applications of my work in proteins. Using https://www.rcsb.org/, how do I find proteins that have similar (but perhaps not the ...
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Proteins with one SS bond?

I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on https://www.rcsb.org/, but no such option, at least I could not find ...
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17 views

Post docking evaluation

What to do after protein-ligand docking? Is there any necessary or enhancement step recommended after docking to validate the confirmation of highest score is the best? For your information, I am ...
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How to find Wild Type (WT) protein structure on Protein Data Bank (PDB)?

Currently, I am working on Galactose oxidase enzyme for protein docking and I am totally new to it. I have to study how mutation on specific residue will make mutated galactose oxidase better than the ...
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Why is it necessary to add hydrogen and delete water before protein-ligand docking?

What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
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How to define TMH boundaries from structures in OPM at the sequence level

I am trying to find which are the transmembrane residues in a given structure. OPM uses PPI to orient TMPs in a membrane space. OPM looks to have the boudnaries at the atomistic level from their ...
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Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
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What is a sensible forcefield choice for membrane proteins when using PDB2PQR?

I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. There are no lipids in the structure. PDB2PQR has predefined options of amber, charmm, parse, tyl06, ...
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Reconstruct a protein's 3D structure from a pair-wise distance matrix

What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues? I think the question is self-explanatory. I know of this method but it seems that it uses ...
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53 views

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
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56 views

Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms. Specifically, I'd like to determine the ...
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Label protein strucuture residues in Chimera

I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Columbic electrostatic potential. I have opened them in two separate windows for comparison....
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If I modify a PDB file with a specific mutation, how to minimize energy?

I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized. Is it valid to modify the reference PDB file (I mean by hand) to match ...
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Finding new drug-protein targets/interactions using a known one as base

Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not? If anyone ...
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156 views

What are the differences between “Site” and “CONECT” in a PDB file

The CONECT section in a PDB file describes atomic connectivity. The SITE section describes (among other characteristics), ...
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392 views

Is there a standard way to clean a PDB file and re-number its residues?

Is there a pre-existing tool which will tidy up the numbering of a PDB file? Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
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Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
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Can I batch output the graph of Secondary Structure in VMD Timeline analysis?

I am using the VMD software, and use "Extension - Analysis - Timeline - Calculate - Calc. Sec. Structure" to visualise the secondary structure of my trajectories. I need to screenshot to get the ...
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“No records to view” error in the “Drug and Drug Target Mapping” PDB's search engine

I'm using the "Drug and Drug Target Mapping" search engine (http://www.rcsb.org/pdb/ligand/drugMapping.do). I've noticed that there are some drugs (generic names) that if they appear in the query, the ...
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107 views

Cross-reference with PDB database

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
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Protein fold pathfinding?

This is probably a long-shot since it would be so dependent upon the underlying folding algorithms. Are there known algorithms for mapping the path followed in a protein folding simulation when you ...
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Folded Protein Chunk Dimensional Classification?

Are there known scales and precisions required of dimensions for the classification of folded proteins given a starting chunk as defined by something like the clustering functionality of MSM Builder? ...
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Chimera Alignments

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want ...
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1answer
51 views

How can I compare structures of proteins responsible for dehydration tolerance in plants?

For my undergraduate research project, I'm trying to compare the structures of some proteins, specifically transcription factors crucial for dehydration tolerance in plants, in the hope of finding ...
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Differences between TM and GDT-TS scores for structure comparison

What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
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Do any publicly available databases detail protein structure and functional domains?

I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
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Minimizing Grid Mapping time of Protein Surface

This is an interesting problem - I was wondering if anyone has a creative solution. So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
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115 views

Tool for predicting interactions in the cell

What tools are available to predict, based on the structure of a certain protein, its interactions within a cell? For example, I am considering the split GFP protein and I am trying to predict if ...
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187 views

Best distance parameter for estimating physical interaction between residues in a PDB file

We can calculate the distance between residues in a PDB file regarding different parameters like closest atoms, alpha carbon, beta carbon, centroid and etc. Which one of these parameters are better to ...
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How can we find the distance between all residues in a PDB file?

If we have a PDB structrure, how can we find residues physically interacting with each other in space? I know that we must find the distance between residues and if the distance is less than 5-6 ...
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how to find the bound form of an enzyme structure?

For my undergraduate research I'm looking for a database that gives the bound form of a particular protein structure. Is there any database that provide us with such data? So far I've found following ...
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270 views

Finding residues physically interacting in a PDB structure and sequence related to that structure [duplicate]

I am going to describle the problem completely. First I should say that there are two kinds of interactions: transient and stable interactions. We are supposed to work on stable interaction like ...
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Getting structure and sequence related to PDB IDs

I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer. In a heterodimer there are two chains ...
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65 views

Is there a software or web server to calculate thermodynamic parameter enthalpy change of cellulase?

I want to calculate thermodynamic paremeter enthalpy change of cellulase, but I don't know what software can do this work. Please tell me, thank you very much !
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How to select high quality structures from the Protein Data Bank?

Models of structures deposited in the Protein Data Bank vary in the quality, depending both on the data quality and expertise and patience of the person who built the model. Is there a well-accepted ...
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Phyre2 vs ITasser, completely different models generated

Does anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am ...