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• Converting Sdf Format To Pdb Format
  How to I convert a 2D sdf format file into a correct 3D pdb format structure (to be used in docki...
• Downloading all pdb files from RCSB
  Hello. Is there any way to download all the proteins 3D structure from rcsb? I want to download a...
• 3D to voxel
  How do i generate a voxel matrix from a 3D structure of a gene present in .pdb format?
• Is There A Software For 3D Printing Of Pdb Structures?
  I have just learned that we have a 3D printer, unfortunately I don't know the model and make. I w...
• Sequence To Structure
  Hi, does anyone know a way to generate the 3d linear structure of a protein given the sequence, n...
• Database Or Repository Containing All Protein Structures From Pdb In Docking Ready Format (Pdb, Mol2)
  I have some ligand structures and I would like to which proteins it could interact to. For that I...
• Equirectangular projection of 3D structure of gene
  Does anyone have any code to basically get the equirectangular projection of the 3 D structure of...
• possible method to draw a 3D structure by PDB or Blast or swiss model
  I think Homology modeling predicts the 3D structure compared to protein threading, but I do have ...
• Spherical coordinates of 3D structure of gene
  Does anyone have any code to get the spherical coordinates of the 3D structure of gene(3D structu...
• Protein Structure Reconstruction
  I am new to protein structure reconstruction. Can anyone help to find a best program or tools to ...
• change the helix structure to b -sheet in pdb file format
  I HAVE A PDB FILE FORMAT OF MY PROTEIN AND I WANT TO CHANGE THE 2 FRAGMENTS WITH HELIX STRUCTURE...
• Protein 3D Structure Principal Axes
  Can anyone suggest some free software for calculating the principal axes for a protein 3d structu...
• What is the best accurate method to predict the structure of a fusion protein with a rigid linker between them
  Hi, I'm very new to bioinformatic. I have 2 protein (that already have PDB file) and I want to f...
• Structures Of Cyclodextrin Complexed With Small Ligands
  For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, m...
• VCF +PDB for protein structure prediction
  Hello! I have a set of PDB files for small proteins as well as ~600 VCF (mostly SNPs and short i...
• 3D modelling of protein
  As we know that coils and loops are evolutionary variable regions where mutations,deletions, and ...
• How well would NAMD work for de novo structure prediction of small peptides?
  I have several hundred small peptide (10-20aa) sequences that came out of a screen. I want to get...
• How to "linearize" or "unfold" a PDB format structure to secondary structure?
  Hi all, I need a quick hack for the following problem: I have a protein structure (generated by ...
• Pymol/Vmd - Switch To Atomic Level
  Hello, I'm trying to figure out the structure of a protein. So I installed the programs Pymol an...
• How To Convert Pdb.Gz To Pdb Directly In In Java
  import java.util.Map; import javax.swing.text.Position; import org.biojava.bio.structure.*; i...
• Retrieve all distinct domains from PDB (or lots of them)?
  I would like to understand how the PDB manages domains. My understanding is that the internal fol...