Hot answers tagged

12 votes
Accepted

How I can analyze and present docking results?

You can analyze your docking results in two ways. First way is looking for the score function your program uses. For some score functions, lower value indicates better interactions and for others, ...
user avatar
  • 18.5k
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 ...
user avatar
  • 18.5k
10 votes

What are some free programs to do docking?

CDOCKER CDOCKER is docking program developed by the Brooks Lab and it works with CHARMM. CHARMM does have a free version named charmm. The difference is no DOMDEC or GPU high performance modules. Pros:...
user avatar
  • 1,486
8 votes
Accepted

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 ...
user avatar
  • 18.5k
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 ...
user avatar
  • 18.5k
8 votes
Accepted

Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?

Changing the force field parameters is not a good/recommended approach. This is due to the high number of parameters you have to know. Many of them, you cannot obtain from experimental data. Instead, ...
user avatar
  • 18.5k
7 votes

What are some free programs to do docking?

AUTODOCK VINA Autodock Vina (associated paper) is quite old and hasn't been updated since 2011 but is still commonly used. Autodock Vina has flexible ligands by default, although selected (or all) ...
user avatar
7 votes

How I can analyze and present docking results?

Docking results can be analyzed in a number of ways by looking at various geometric parameters, such as a distances, angles and dihedrals. These are then typically compared against "ideal" values, ...
user avatar
  • 1,486
7 votes

How to initiate protein-ligand docking with MD simulation tools

You can do it either way. You need to give predocked files to GROMACS/Amber for running protein-ligand complex molecular simulations. Also have a look at HADDOCK web server for predocking. Place the ...
user avatar
  • 974
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 ...
user avatar
  • 1,429
6 votes
Accepted

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 (...
user avatar
  • 974
6 votes

Docked pose and energy minimization

One way these calculations are performed is using MD and implicit solvent calculations. The general procedure for these simulations are: Perform simulations and get frames Perform implicit solvent ...
user avatar
  • 1,486
6 votes

MM-GBSA from Induced Fit Docking on Maestro

The Prime MM-GBSA panel is bellow. As you can see, the first section is about choosing the structures to calculate the MM-GBSA energy. The marked option works only for pose viewer files. IFD don't ...
user avatar
  • 18.5k
6 votes

What are some free programs to do docking?

MEGADOCK Megadock (associated paper) is a free GPU-enabled docking program for rigid protein–protein docking. Pros: Very fast. Can screen thousands of structures in a few hours. Cons: Both ligand and ...
user avatar
6 votes

How to initiate protein-ligand docking with MD simulation tools

Docking and Molecular dynamics are two very different process. In docking, you will need the ligand (normally in a separate file), the protein (can be in a separate file too), and the information ...
user avatar
  • 18.5k
5 votes

What are some free programs to do docking?

PLANTS PLANTS uses a class of stochastic optimization algorithms called ant colony optimization (ACO). Feature list: ...
user avatar
  • 18.5k
5 votes

What are some free programs to do docking?

FLEXPEPDOCK FlexPepDock (associated paper) is part of the Rosetta toolkit and useful for peptide–protein docking. Pros: Peptide is fully flexible. Makes use of Rosetta's excellent protein modeling ...
user avatar
5 votes

What are some free programs to do docking?

1. Ab-initio protein--protein docking: GRAMM (=Global Range Molecular Modeling) Performs rigid-body docking based on the shape complementarity and Miyazawa-Jernigan contact potentials; Exhaustively ...
user avatar
  • 301
5 votes

What are the factors to consider before docking 2 proteins?

Another factor to consider might be blind docking or targeted. In this latter, only a region indicated on protein is targeted. In blind docking, the ligand will bind wherever suited on the protein ...
user avatar
  • 1,301
5 votes

Docking validation RMSD over 3, How can I fix it?

You cannot "fix" it. As a RMSD value is considered good below $2 \overset{\circ}{\mathrm{A}}$, you can try one of this two methods to obtain better RMSD: Repeat the docking calculation ...
user avatar
  • 18.5k
5 votes

Protein structure prediction

In the past I had the same question and after a long search I found that every two year there is a worldwide competition to assess the quality of 3D structure prediction of proteins. In the past the ...
user avatar
  • 1,429
5 votes

Protein structure prediction

Your protocol is right and rigorous in the sense as if you don't have the crystal structure of your protein and want to do some predictions, them the only way is using homology modeling. I am not a ...
user avatar
  • 18.5k
5 votes
Accepted

How can I get Vina to recognise boron atoms?

As Vina (and other docking software) uses Molecular Mechanics (force-fields) to optimize/score the ligand/protein, in order to use not predefined atoms, you need to generate, by yourself, the force-...
user avatar
  • 18.5k
4 votes
Accepted

How to interpret the affinity in a protein docking - ligand

In a molecular docking, the affinity between a protein and a ligand is determined using what is called score functions. Each docking software has its own score function. These score functions are ...
user avatar
  • 18.5k
4 votes

How can I validate docking result without a co-crystallized ligand?

Using different score functions One way to validate the docking results is scoring your poses using a different score function. You will need to use one of this two methods: Use another docking ...
user avatar
  • 18.5k
4 votes
Accepted

How to compare structural results by superposition and compute RMSD to validate docking?

Here are the steps to validate your docking protocol (not your docking results): (Note: this is one way to do the validation, not the only one) Download a crystal structure of a complex (ligand/...
user avatar
  • 18.5k
4 votes

What novel drugs are developed via CADD?

In my opinion, there are no new drug molecules totally designed by computer. These designed drug molecules with CADD must be tested with many experiments. Here is a review paper about the current and ...
user avatar
  • 13.6k
4 votes

Why am I losing bonds when I use PACKMOL on two proteins?

Packmol is used to pack molecules into a given box at random positions and with random rotations. If you want the spike glycoprotein to be attached to the membrane, you should probably prepare a new ...
user avatar
  • 14.2k
4 votes

Docking proteins with glycans

The main issue here is not about the type of ligands (glycans) even when it is known that there are force fields that are specific for each type of system. The main issue is about how flexible and big ...
user avatar
  • 18.5k
4 votes

Why are ligands restrained when simulating a protein-ligand complex with MD?

The cause to use restrains is due to a previous knowledge (i.e. experimental) of system behavior/characteristics that you want to include/retain/reproduce in your simulations. In the case of protein-...
user avatar
  • 18.5k

Only top scored, non community-wiki answers of a minimum length are eligible