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    Apuntes

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    Paula Delgado
    The document discusses how to address a non-integral total charge error when docking proteins in Autodock. It recommends using the "Edit-->Charges-->Check Totals on Residues" option in Autodock to spread the charge deficit/surplus over many atoms to end up with an integral charge. It also provides some additional docking software and resources for protein-protein docking.

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    Apuntes

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    Paula Delgado
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    The document discusses how to address a non-integral total charge error when docking proteins in Autodock. It recommends using the "Edit-->Charges-->Check Totals on Residues" option in Autodock to spread the charge deficit/surplus over many atoms to end up with an integral charge. It also provides some additional docking software and resources for protein-protein docking.

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    The document discusses how to address a non-integral total charge error when docking proteins in Autodock. It recommends using the "Edit-->Charges-->Check Totals on Residues" option in Autodock to spread the charge deficit/surplus over many atoms to end up with an integral charge. It also provides some additional docking software and resources for protein-protein docking.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as DOC, PDF, TXT or read online from Scribd
    Download as doc, pdf, or txt
    92 views3 pages

    Apuntes

    Uploaded by

    Paula Delgado
    The document discusses how to address a non-integral total charge error when docking proteins in Autodock. It recommends using the "Edit-->Charges-->Check Totals on Residues" option in Autodock to spread the charge deficit/surplus over many atoms to end up with an integral charge. It also provides some additional docking software and resources for protein-protein docking.

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    Download as DOC, PDF, TXT or read online from Scribd
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    http://autodock.1369657.n2.nabble.com/ADL-total-ligand-charge-error-td2283263.

    html
    When preparing your "ligand' in ADT, and after adding charges, go to Edit-->Charges-->Check Totals on Residues. This should give you an option to spread the charge deficit/surplus over many atoms so that you end up with an integral charge. On Friday 06 February 2009 03:43:01 am Gav wrote: > Hi I am docking a protein to a protein and get > > autodock4: *** WARNING! Non-integral total charge (-4.967 e) on ligand! > *** > > ad4 then stops. Can anyone help? > gav

    http://mgl.scripps.edu/people/gmm/index.html

    http://mgl.scripps.edu/

    3D-Dock http://www.sbg.bio.ic.ac.uk/docking/ DOCK http://dock.compbio.ucsf.edu/DOCK_6/index.htm ZDOCK

    http://zdock.umassmed.edu/software/ ZDOCK 1.3: This version uses grid-based shape complementarity, desolvation, and electrostatics in the target function. Please reference: Chen R, Weng Z (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics, Proteins 47:281-294 for usage of the software or decoy set of ZDOCK 1.3. ZDOCK 2.1: This version uses a novel pairwise shape complementarity target function. Please reference: Chen R, Weng Z (2003) A Novel Shape Complementarirty Scoring Function for ProteinProtein Docking, Proteins 51:397-408 for usage of the software or decoy set of ZDOCK 2.1. ZDOCK 2.3: This version uses pairwise shape complementarity, desolvation and electrostatics in the target function. Check out its performance in a worldwide blind test, CAPRI. Please reference: Chen R, Li L, Weng Z (2003) ZDOCK: An Initial-stage Protein Docking Algorithm, Proteins 52: 80-87 for usage of the software or decoy set of ZDOCK 2.3. ZDOCK 3.0: This version uses pairwise shape complementarity, IFACE and electrostatics in the target function. It has been shown to have improved success with docking Benchmark 2.0 versus ZDOCK 2.3. Please reference: Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z Integrating Statistical Pair Potentials into Protein Complex Prediction. Proteins 69(3): 511-520. ZDOCK 2.3.3 and ZDOCK 3.0.2: These versions utilize the Conv3D library and other optimizations to improve speed and memory usage. ZDOCK 2.3.2 is based on the scoring function of ZDOCK 2.3, and ZDOCK 3.0.2 is based on the scoring function of ZDOCK 3.0. Please reference: Pierce BG, Hourai Y, Weng Z (2011). Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library. PLoS One 6(9): e24657.

    ZRANK
    ZRANK is a program for reranking sets of initial-stage docking predictions using an optimized energy-based function. It has been tested using ZDOCK 2.1, 2.3, and 3.0 predictions for Benchmark 2.0, and significantly improved the success rates over the initial ZDOCK rankings. More about ZRANK can be found in this paper. ZRANK is available for download on several platforms:

    Docking Sites

    ZDOCK, RDOCK

    AutoDock Bielefeld Protein Docking Vajda Lab DOCK DOT FTDock, RPScore and MultiDock GRAMM Hex 3.0 ICM Protein-Protein docking KORDO MolFit MPI Protein Docking Nussinov-Wolfson Structural Bioinformatics Group

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