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Protocol
Software and Databases for Protein–Protein Docking
Protein–protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computation...
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Article
Retraction Note: IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance
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Article
RETRACTED ARTICLE: IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance
Isoprenoids are vital for all organisms, in which they maintain membrane stability and support core functions such as respiration1. IspH, an enzyme in the methyl erythritol phosphate pathway of isoprenoid synthes...
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Article
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4
Macrocycles represent a potentially vast extension of drug chemical space still largely untapped by synthetic compounds. Sampling of flexible rings is incorporated in the ICM-dock protocol. We tested the abili...
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Article
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3
In context of D3R Grand Challenge 3 we have investigated several ligand activity prediction protocols that combined elements of a physics-based energy function (ICM VLS score) and the knowledge-based Atomic Pr...
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Article
Open AccessFunctional Antibody Response Against V1V2 and V3 of HIV gp120 in the VAX003 and VAX004 Vaccine Trials
Immunization with HIV AIDSVAX gp120 vaccines in the phase III VAX003 and VAX004 trials did not confer protection. To understand the shortcomings in antibody (Ab) responses induced by these vaccines, we evaluat...
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Article
Open AccessLigand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. ...
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Article
Open AccessBioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools i...
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Article
Docking and scoring with ICM: the benchmarking results and strategies for improvement
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The I...
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Protocol
Loop Simulations
Loop modeling is crucial for high-quality homology model construction outside conserved secondary structure elements. Dozens of loop modeling protocols involving a range of database and ab initio search algori...
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Article
Interactive JIMD articles using the iSee concept: turning a new page on structural biology data
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Article
Open AccessLigand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly ...
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Article
Conserved structural elements in the V3 crown of HIV-1 gp120
The V3 crown region of HIV-1 gp120 is involved in binding to co-receptors CCR5 and CXCR4, and show high sequence variability. Structural work with cross-clade neutralizing antibodies in complex with V3 peptide...
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Article
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple con...
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Article
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
Essential for viral replication and highly conserved among poxviridae, the vaccinia virus I7L ubiquitin-like proteinase (ULP) is an attractive target for development of smallpox antiviral drugs. At the same time,...
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Article
Waltzing transporters and 'the dance macabre' between humans and bacteria
Multidrug-resistance (MDR) efflux pumps are membrane transporter proteins that have a broad-spectrum of substrate specificity.
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Article
Comparative study of several algorithms for flexible ligand docking
We have performed a comparative assessment of several programs for flexible molecular docking: DOCK 4.0, FlexX 1.8, AutoDock 3.0, GOLD 1.2 and ICM 2.8. This was accomplished using two different studies: dockin...
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Article
Open AccessStructural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine
Nicotine is a psychoactive drug presenting a diverse array of biological activities, some positive, such as enhancement of cognitive performances, others negative, such as addiction liability. Ligands that dis...
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Article
Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy
The fundamental event in biological assembly is association of two biological macromolecules. Here we present a successful, accurate ab initio prediction of the binding of uncomplexed lysozyme to the HyHel5 antib...
