User: ramachandranakash1994

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Posts by ramachandranakash1994

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In ZRank scoring function, which gets a higher rank : The decoy with lower ZRank score or the one with a higher ZRank score
... I am ranking a set of protein-protein decoys generated by docking 2 proteins. For ranking I am using the scoring function ZRank. I am not sure which decoy gets the higher rank: the one with lower ZRank score or the one with the higher ZRank score. For example: Decoy 1: ZRank score = -170 Decoy 2: ...
zrank docking scoring functions written 2.9 years ago by ramachandranakash19940 • updated 3 months ago by Biostar ♦♦ 20
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Addition of polar hydrogens to the unbound structures before ranking by ZRank
... **I need urgent help with this please! This is for a project I have to submit in a few days** I have generated protein-protein decoys using ZDock and I am trying to rank them using ZRank scoring function. I was not clear about what was mentioned in the ZRank read-me file. After generating the decoy ...
zrank scoring funciton zdock docking written 2.9 years ago by ramachandranakash19940
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Addition of polar hydrogens to the unbound structures before ranking by ZRank
... I have generated protein-protein decoys using ZDock and I am trying to rank them using ZRank scoring function. I was not clear about what was mentioned in the ZRank read-me file. After generating the decoys using ZDock, do I add polar hydrogens to all of the decoys or only the unbound structures ? ...
zrank scoring funciton zdock docking written 2.9 years ago by ramachandranakash19940
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Comment: C: Capri Criteria For Evaluating Docked Protein Complexes
... @ João Rodrigues - I am new to programming and do not understand the working of NeighborSearch. Would you be able to give me the code to find all of the interface residues (as defined by you) between 2 chains in heterodimeric proteins? ...
written 3.0 years ago by ramachandranakash19940
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Comment: C: Syntax For Neighborsearch Module In Biopython
... Hi I have large number of hetero-dimeric proteins. I need to check for all atoms of chain A for which atoms of chain B are within 10Å and need to obtain the list of residue numbers of those atoms as output. I am new to programming and I do not know how to write the code for this using the NeighborS ...
written 3.0 years ago by ramachandranakash19940
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How to select an unbound structure for a bound protein from multiple options in protein-protein docking
... I am doing a project on protein-protein docking. My objective to test how good a docking algorithm is. For this I will be doing unbound docking of hetero-dimeric proteins. For every hetero-dimer, I have multiple unbound structures for each of the 2 chains. How do I select 1 unbound structure from t ...
protein-protein docking docking written 3.0 years ago by ramachandranakash19940
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Comment: C: Randomizing side chain orientation of a protein structure
... Thank you! I have heard that the biological structure as found in a PDB file need not necessarily be the structure of least energy. My question is would just a minimization of the energies of both chains be sufficient to randomize all of the surface side chains? I want to remove any native-complex b ...
written 3.0 years ago by ramachandranakash19940
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Changing the conformation of bound protein chain to its unbound state
... If I want to carry out an unbound docking of the 2 chains of a hetero-dimeric protein but the individual unbound structures are not available, how do I change the structure of the bound partners to remove any native-complex structure bias that the 2 chains might have ? I am using ZDock, a rigid-bod ...
protein-protein docking written 3.0 years ago by ramachandranakash19940 • updated 3.0 years ago by Biostar ♦♦ 20
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Randomizing side chain orientation of a protein structure
... Hello, I have the quaternary structures of hetero-dimeric proteins. I am trying to separate the 2 chains of each protein complex and dock them. Prior to docking I have to randomize the side chain orientation of all amino acids in both the chains of each of the protein complexes. Is there any softw ...

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