{"id":15655268,"url":"https://github.com/rasbt/hbind","last_synced_at":"2025-10-05T12:37:54.732Z","repository":{"id":66172048,"uuid":"107732634","full_name":"rasbt/Hbind","owner":"rasbt","description":"Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. 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Kuhn (2018) “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes” Journal of Computer-Aided Molecular Design. *Journal of Computer-Aided Molecular Design* (accepted manuscript) [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/02/05/260612)]\n\nCode Repository: https://github.com/psa-lab/Hbind  \nDocumentation: [https://psa-lab.github.io/Hbind](https://psa-lab.github.io/Hbind)\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n---\n\n![](docs/sources/images/1kpf_interact.png)\n\n[Interactions between an PKCI-substrate analog ([1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf))  with its ligand (adenosine monophsophate) via [HbindViz](https://github.com/rasbt/HbindViz) and [PyMOL](https://pymol.org); hydrogen atoms not shown]\n\n---\n\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n## Installation\n\nInstalling Hbind requires [Perl](https://www.perl.org) and the [GCC](https://gcc.gnu.org) compiler, both of which come pre-installed with most Unix- and Linux-based operating systems.\n\nTo install Hbind, simply download this repository, unpack it, and navigate into the main Hbind folder. Then, execute the following command in your terminal:\n\n    perl install_hbind.pl\n\nUpon successful installation, the Hbind software will be ready to use from the `bin/` subdirectory. To show the help and usage menu execute execute the following command in your terminal:\n\n    ./bin/hbind -h\n\n\u003cbr\u003e\n\n```\nHBIND Version: 1.0.0\n\nDocumentation: http://psa-lab.github.io/Hbind\nRaschka, Wolf, Bemister-Buffington, Kuhn (2018)\nProtein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)\n\n\nUSAGE:\n-p STRING     Path to protein PDB file\n-l STRING     Path to ligand mol2 file (in docked conformation)\n-s            Include saltbridges in the output\n-t            Include a summary table in the output\n```\n\n\n\nPlease see the \"Usage\" section below for more information on how to use Hbind.\n\n\u003cbr\u003e\n\n## Usage\n\nTo execute Hbind, please navigate to its main directory from where you installed it and run the following command to identify the hydrogen bonds in a protein ligand interface:\n\n    ./bin/hbind -p ./example_files/1KPF.pdb \\\n    -l ./example_files/1KPF_AMP.mol2 \n\nHere, 1KPF.pdb is an excerpt from the PDB structure [1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf) (PKCI-substrate analog) with its ligand `1KPF_AMP.mol2` (adenosine monophsophate). The structures are provided in Hbind's subdirectory \"[example_files/](./example_files)\".\n\n***Before you run Hbind, please make sure that you provide the protein structure in PDB format and the ligand structure in MOL2 format, and please ensure that the ligand's protonation state (hydrogen assignment) is correct.***\n\nTo protonate a ligand, tools such as [OpenEye MolCharge](https://docs.eyesopen.com/quacpac/molchargeusage.html) can be used. However, it is recommended to protonate a ligand in presence of its protein environment, for example, by using tools such as [What If](http://swift.cmbi.ru.nl/whatif/) or [Yasara OptHyd](http://www.yasara.org/features.htm).\n\nAfter running the command from the beginning of this section, the following output should be displayed:\n\n```\nHBIND Version: 1.0.0\n\nDocumentation: http://psa-lab.github.io/Hbind\nRaschka, Wolf, Bemister-Buffington, Kuhn (2018)\nProtein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)\n\nLigand file: /Users/sebastian/code/hbind/example_files/1KPF_AMP.mol2\nProtein file: /Users/sebastian/code/hbind/example_files/1KPF.pdb\n\n++++++++++++++++++++++++++++++++ HBind Interaction Table ++++++++++++++++++++++++++++++++\n#            | Ligand Atom -- Protein  Atom | Bond                D-H-A  Lig.-Prot.\n#            |  #  TYPE    -- RES  CH_ID  RES_NO  A_TYPE | DIST.  ANGLE  INTERACTION\n| hbond     1   2  O.2     -- ASN  A       99     ND2      2.911  174.0  Acceptor - Donor\n| hbond     2   3  O.3     -- SER  A      107     N        2.802  166.8  Acceptor - Donor\n| hbond     3   3  O.3     -- VAL  A      108     N        3.031  178.8  Acceptor - Donor\n| hbond     4   4  O.3     -- HIS  A      112     NE2      2.593  163.1  Acceptor - Donor\n| hbond     5   4  O.3     -- HIS  A      114     NE2      2.581  140.4  Acceptor - Donor\n| hbond     6  10  O.3     -- ASP  A       43     OD2      2.714  167.1  Donor - Acceptor\n| hbond     7  12  O.3     -- ASP  A       43     OD1      2.607  154.1  Donor - Acceptor\n| hbond     8  22  N.ar    -- ILE  A       44     N        3.156  154.9  Acceptor - Donor\n```\n\nTo include salt bridges in the listing, you can use the `-s` option as shown below:\n\n    ./bin/hbind -p ./example_files/1KPF.pdb \\\n    -l ./example_files/1KPF_AMP.mol2 -s\n\n```\nHBIND Version: 1.0.0\n\nDocumentation: http://psa-lab.github.io/Hbind\nRaschka, Wolf, Bemister-Buffington, Kuhn (2018)\nProtein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)\n\nLigand file: /Users/sebastian/code/hbind/example_files/1KPF_AMP.mol2\nProtein file: /Users/sebastian/code/hbind/example_files/1KPF.pdb\n\n++++++++++++++++++++++++++++++++ HBind Interaction Table ++++++++++++++++++++++++++++++++\n#            | Ligand Atom -- Protein  Atom | Bond                D-H-A  Lig.-Prot.\n#            |  #  TYPE    -- RES  CH_ID  RES_NO  A_TYPE | DIST.  ANGLE  INTERACTION\n| hbond     1   2  O.2     -- ASN  A       99     ND2      2.911  174.0  Acceptor - Donor\n| hbond     2   3  O.3     -- SER  A      107     N        2.802  166.8  Acceptor - Donor\n| hbond     3   3  O.3     -- VAL  A      108     N        3.031  178.8  Acceptor - Donor\n| hbond     4   4  O.3     -- HIS  A      112     NE2      2.593  163.1  Acceptor - Donor\n| hbond     5   4  O.3     -- HIS  A      114     NE2      2.581  140.4  Acceptor - Donor\n| hbond     6  10  O.3     -- ASP  A       43     OD2      2.714  167.1  Donor - Acceptor\n| hbond     7  12  O.3     -- ASP  A       43     OD1      2.607  154.1  Donor - Acceptor\n| hbond     8  22  N.ar    -- ILE  A       44     N        3.156  154.9  Acceptor - Donor\n| saltb     1   2  O.2     -- HIS  A      114     NE2      4.245  N/A    Acceptor - Donor\n| saltb     2   3  O.3     -- HIS  A      112     NE2      3.382  N/A    Acceptor - Donor\n| saltb     3   4  O.3     -- HIS  A      114     ND1      4.462  N/A    Acceptor - Donor\n| saltb     4  10  O.3     -- ASP  A       43     OD1      3.395  N/A    Donor - Acceptor\n| saltb     5  12  O.3     -- ASP  A       43     OD2      3.607  N/A    Donor - Acceptor\n```\n\nFor additional information, i.e. a summary talbe that includes the number of hydrophobic contacts or [SLIDE](http://www.kuhnlab.bmb.msu.edu/software/slide/) docking scores, provide the `-t` flag:\n\n    ./bin/hbind -p ./example_files/1KPF.pdb \\\n    -l ./example_files/1KPF_AMP.mol2 -s -t\n\n```\nHBIND Version: 1.0.0\n\nDocumentation: http://psa-lab.github.io/Hbind\nRaschka, Wolf, Bemister-Buffington, Kuhn (2018)\nProtein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)\n\nLigand file: /Users/sebastian/code/hbind/example_files/1KPF_AMP.mol2\nProtein file: /Users/sebastian/code/hbind/example_files/1KPF.pdb\n\n+++++++++++++++++ Summary +++++++++++++++++++\n| Protein-Ligand Hydrophobic Contacts :    39\n| Protein-Ligand H-bonds              :     8\n| Protein-Ligand Salt-bridges         :     5\n| Metal-Ligand Bonds                  :     0\n| SLIDE OrientScore                   : -8.787\n| SLIDE AffiScore (heavy atoms)       : -0.102\n| SLIDE AffiScore                     : -7.557\n\n++++++++++++++++++++++++++++++++ HBind Interaction Table ++++++++++++++++++++++++++++++++\n#            | Ligand Atom -- Protein  Atom | Bond                D-H-A  Lig.-Prot.\n#            |  #  TYPE    -- RES  CH_ID  RES_NO  A_TYPE | DIST.  ANGLE  INTERACTION\n| hbond     1   2  O.2     -- ASN  A       99     ND2      2.911  174.0  Acceptor - Donor\n| hbond     2   3  O.3     -- SER  A      107     N        2.802  166.8  Acceptor - Donor\n| hbond     3   3  O.3     -- VAL  A      108     N        3.031  178.8  Acceptor - Donor\n| hbond     4   4  O.3     -- HIS  A      112     NE2      2.593  163.1  Acceptor - Donor\n| hbond     5   4  O.3     -- HIS  A      114     NE2      2.581  140.4  Acceptor - Donor\n| hbond     6  10  O.3     -- ASP  A       43     OD2      2.714  167.1  Donor - Acceptor\n| hbond     7  12  O.3     -- ASP  A       43     OD1      2.607  154.1  Donor - Acceptor\n| hbond     8  22  N.ar    -- ILE  A       44     N        3.156  154.9  Acceptor - Donor\n| saltb     1   2  O.2     -- HIS  A      114     NE2      4.245  N/A    Acceptor - Donor\n| saltb     2   3  O.3     -- HIS  A      112     NE2      3.382  N/A    Acceptor - Donor\n| saltb     3   4  O.3     -- HIS  A      114     ND1      4.462  N/A    Acceptor - Donor\n| saltb     4  10  O.3     -- ASP  A       43     OD1      3.395  N/A    Donor - Acceptor\n| saltb     5  12  O.3     -- ASP  A       43     OD2      3.607  N/A    Donor - Acceptor\n```\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n\n\n\n## Hydrogen bond rules\n\nHbind's rules for identifying hydrogen bonds protein-ligand interfaces are based on the criteria by Ippolito et al. [1] and McDonald and Thornton [2].\n\n#### Hydrogen bond criteria:\n\n- Hydrogen to acceptor distance: 1.5-2.5 Å\n- Donor to acceptor distance: 2.4-3.5 Å\n- Donor-H-acceptor angle (θ): 120-180°\n- Pre-acceptor–acceptor–H angle (φ): 90-180°\n\n(Hydrogen bonds must meet all of these criteria.)\n\n#### Criteria for metal interactions:\n\n- Lone pair atom distance to K or Na: 2.0-2.9 Å\n- Lone pair atom distance to Ca, Co, Cu, Fe, Mg, Mn, Ni, or Zn: 1.7-2.6 Å\n\nAdditional command line options are available to list longer-range salt bridge interactions (up to 4.5 Å) and the number of hydrophobic contancts between protein and ligand atoms.\n\n\n[1] Ippolito, Joseph A, Richard S Alexander \u0026 David W Christianson. 1990. Hydrogen bond stereo-chemistry in protein structure and function. *Journal of Molecular Biology* 215(3). 457–471.   \n[2] McDonald, Ian \u0026 Janet M Thornton. 1994. Atlas of side-chain and main-chain hydrogen bonding. http://www.biochem.ucl.ac.uk/bsm/atlas: Biochemistry and Molecular Biology Department, University College London.\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n\n## Hbind tools\n\n###  Protein Recognition Index (PRI) \n\nSoftware for assessing the native-likeness of designed or predicted protein-ligand interfaces, which can be used to guide protein mutagenesis and ligand design.\n\n- [https://psa-lab.github.io/protein-recognition-index/](https://psa-lab.github.io/protein-recognition-index/)\n\n### Hbind Interaction Viz\n\nA program for creating PyMOL H-bond interaction views from Hbind tables.\n\n- [http://psa-lab.github.io/HbindViz](http://psa-lab.github.io/HbindViz)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fhbind","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frasbt%2Fhbind","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fhbind/lists"}