GRAMM-X public web server for protein–protein docking

By A. Tovchigrechko, Ilya A. Vakser. Nucleic Acids Res., 2006

786 citations recorded by the source corpus.

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8e940043345a29c57e47f488be50c9f03fe28b21

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The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Brian G. Pierce
2. Jeffrey J. Gray
3. Shengyou Huang
4. Zhiping Weng
5. Yumeng Yan
6. Joël Janin
7. Ranjit Prasad Bahadur
8. Huanyu Tao

In Molecular Biology

1. Shengyou Huang
2. Brian G. Pierce
3. Alexandre M. J. J. Bonvin
4. Zhiping Weng
5. Jeffrey J. Gray
6. Haim J. Wolfson
7. Xiaoqin Zou
8. Ruth Nussinov

Citations in the corpus

• ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers (2014, methodology): “Contact: brian.pierce@umassmed.edu or zhiping.weng@umassmed.edu Received on November 22, 2013; revised on January 17, 2014; accepted on February 7, 2014”
• HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, neutral): “For years, a number of docking algorithms and their web servers such as ClusPro (10), HADDOCK (11), Roset-taDock server (12), GRAMM-X (13), 3D-Garden (14), HEX server (15), SwarmDock (16), ZDOCK server (17), PatchDock (18), ATTRACT (19), pyDockSAXS (20), In-terEvDock (9) and NPDock (21), have been…”
• InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, neutral): “Attempts to address the limitations of computational docking have led to placing increasing focus on data-driven docking (24) and many servers now allow the user to specify interface residues and/or distance restraints, including ZDOCK, FRODOCK 2.0 (for refinement), pyDockWEB, ClusPro, GRAMM-X, Swar”
• HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “A number of template-free docking servers have been developed and released to the public, such as ATTRACT (5), ClusPro (6), HADDOCK (7), ZDOCK server (8), SwarmDock (9), pyDockSAXS (10), pyDockWeb (11), In-terEvDock2 (12), GRAMM-X (13), RosettaDock server (14), PatchDock (15), Hex server (16), 3D-Ga”
• HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, background): “To make protein–protein docking user-friendly, a number of protein–protein docking servers such as ClusPro (4), HADDOCK (5), RosettaDock server (6), GRAMMX (7), 3D-Garden (8), HEX server (9), SwarmDock (10), ZDOCK server (11), PatchDock (12), ATTRACT (13), pyDockSAXS (14), InterEvDock (15) and HDOCK”
• Protein–protein interaction and quaternary structure (2008, methodology): “Procedures based on that algorithm are implemented in a number of servers : ClusPro (Comeau et al. 2004), SmoothDock, MultiDock (Gabb et al. 1997), Gramm-X (Tovchigrechko & Vakser, 2006).”
• The RosettaDock server for local protein–protein docking (2008, methodology): “Several protein–protein docking servers are available on the Internet, including ClusPro (2), GRAMM-X (3) and ZDOCK (4) based on fast-Fourier transform methods for grid matching; PatchDock and SymmDock (5) based on shape complementarity principles and symmetry restrictions; and Hex based on spherica”
• FireDock: a web server for fast interaction refinement in molecular docking (2008, methodology): “The candidate solutions for FireDock can be generated by rigid-body docking methods, such as PatchDock (10,21), methods that use Fast Fourier Transform (FFT) such as ZDOCK (20,36), GRAMM-X (26), Hex (27), etc.”
• HexServer: an FFT-based protein docking server powered by graphics processors (2010, neutral): “Several FFT-based docking programs have also been made available as web servers e.g. ClusPro (7), GRAMM-X (8) and ZDOCK (9).”