A hierarchical method for molecular docking using cloud computing

Discovering small molecules that interact with protein targets will be a key part of future drug discovery efforts. Molecular docking of drug-like molecules is likely to be valuable in this field; however, the great number of such molecules makes the potential size of this task enormous. In this paper, a method to screen small molecular databases using cloud computing is proposed. This method is called the hierarchical method for molecular docking and can be completed in a relatively short period of time. In this method, the optimization of molecular docking is divided into two subproblems based on the different effects on the protein–ligand interaction energy. An adaptive genetic algorithm is developed to solve the optimization problem and a new docking program (FlexGAsDock) based on the hierarchical docking method has been developed. The implementation of docking on a cloud computing platform is then discussed. The docking results show that this method can be conveniently used for the efficient molecular design of drugs.     

MOLPACK: molecular graphics,for studying the packing of protein molecules in the crystallographic unit cell

A graphics program, MOLPACK, has been developed on the Silicon Graphics IRIS-4D computer system for displaying the packing of proteins in the crystallographic unit cell. In addition to the normal viewing operations of rotation, translation and scaling, the program has the ability to translate molecules along the cell axes while maintaining their crystallographic equivalent positions within the unit cell. This allows the user to observe the packing of protein molecules generated by molecular replacement, to create a new packing model or to locate an unknown molecule. A special feature of the program is that up to four independent molecules can be manipulated in the asymmetric unit.     

SURFNET: A program for visualizing molecular surfaces,cavities, and intermolecular interactions

The SURFNET program generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal cavities and surface grooves within a single molecule. The program is particularly useful in clearly delineating the regions of the active site of a protein. It can also generate 3D contour surfaces of the density distributions of any set of 3D data points. All output surfaces can be viewed interactively, along with the molecules or data points in question, using some of the best-known molecular modeling packages. In addition, PostScript output is available, and the generated surfaces can be rendered using various other graphics packages.     

一种研究蛋白质晶体中分子堆积的图形程序—PACKING

在蛋白质晶体结构研究中常需分析分子在晶胞内的堆积,本文介绍一种用于IRIS-4D计算机的图形软件,可显示分子在晶胞中的堆积图形、计算原子之间的距离和键角等,进行分子置换、模拟不同的分子堆积模型。     

Molecular conformational space analysis using computer graphics: Going beyond FRODO

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.     

A simple method to display molecular orbitals with computer graphics

A computer program named LOBE was developed to draw molecular orbitals as lobes on a graphic display. With this program, any molecular orbital of large molecules can be displayed quickly. This program is suitable not only for general-purpose computers but also for microcomputers. A sample application is used to illustrate the program.     

Systolic Loop Methods for Molecular Dynamics Simulation,Generalised for Macromolecules

Abstract

Systolic loop programs have been shown to be very efficient for molecular dynamics simulations of liquid systems on distributed memory parallel computers. The original methods address the case where the number of molecules simulated exceeds the number of processors used. Simulations of large flexible molecules often do not meet this condition, requiring the three- and four-body terms used to model chemical bonds within a molecule to be distributed over several processors. This paper discusses how the systolic loop methods may be generalised to accommodate such systems, and describes the implementation of a computer program for simulation of protein dynamics. Performance figures are given for this program running typical simulations on a Meiko Computing Surface using different number of processors.     

Ab initio Molecular Electrostatic Potential Grid Maps for Quantitative Similarity Calculations of Organic Compounds

The program MolSim designed to calculate the similarity of different molecules quantitatively in a fast and easy way is described. The molecular similarity is estimated for the molecular shape as well as for the electrostatic potentials of the molecules derived from ab initio calculations. A grid-based method is used to determine the steric and electrostatic similarities between a lead compound and the corresponding test set by calculating the Spearman correlation coefficient. The superpositioning of the molecules was accomplished with the SEAL algorithm incorporating a Monte Carlo simulated annealing approach while preserving the conformational flexibility of the calculated structures.The ability of the program was tested on a set of Sandalwood odour compounds, a class of substances that is difficult to analyse with respect to its structure-activity relationship because of the structural diversity of Sandalwood odour compounds, in contrast to their high selectivity and pronounced structural specificity. The application of the program on a small test set of these compounds showed that the program is able to explain the Sandalwood odour activity correctly.Electronic Supplementary Material available.     

The neuronal growth cone as a specialized transduction system.

Neuronal growth and remodelling are guided by both intracellular gene programs and extracellular stimuli. The growth cone is one site where the effects of these extrinsic and intrinsic factors converge upon the mechanical determinants of cell shape. We review the growth cone as a transduction device, converting extracellular signals into mechanical forces. A variety of soluble, extracellular matrix and membrane bound molecules control growth cone behavior. In addition, GAP-43 is discussed as a possible component of the intraneuronal gene program which modulates growth cone activity. The GTP-binding protein, Go, is a major growth cone membrane protein that may transduce signals not only from outside the cell, but from within as well. This may provide a molecular site in the growth cone for the coordination of a genetic growth program with environmental signals.     

Incorporating replacement free energy of binding‐site waters in molecular docking

Binding‐site water molecules play a crucial role in protein‐ligand recognition, either being displaced upon ligand binding or forming water bridges to stabilize the complex. However, rigorously treating explicit binding‐site waters is challenging in molecular docking, which requires to fully sample ensembles of waters and to consider the free energy cost of replacing waters. Here, we describe a method to incorporate structural and energetic properties of binding‐site waters into molecular docking. We first developed a solvent property analysis (SPA) program to compute the replacement free energies of binding‐site water molecules by post‐processing molecular dynamics trajectories obtained from ligand‐free protein structure simulation in explicit water. Next, we implemented a distance‐dependent scoring term into DOCK scoring function to take account of the water replacement free energy cost upon ligand binding. We assessed this approach in protein targets containing important binding‐site waters, and we demonstrated that our approach is reliable in reproducing the crystal binding geometries of protein‐ligand‐water complexes, as well as moderately improving the ligand docking enrichment performance. In addition, SPA program (free available to academic users upon request) may be applied in identifying hot‐spot binding‐site residues and structure‐based lead optimization. Proteins 2014; 82:1765–1776. © 2014 Wiley Periodicals, Inc.     

The Interactions of Allium sativum leaf agglutinin with a chaperonin group of unique receptor protein isolated from a bacterial endosymbiont of the mustard aphid

The homopteran sucking insect, Lipaphis erysimi (mustard aphid) causes severe damage to various crops. This pest not only affects plants by sucking on the phloem, but it also transmits single-stranded RNA luteoviruses while feeding, which cause disease and damage in the crop. The mannose-binding Allium sativum (garlic) leaf lectin has been found to be a potent control agent of L. erysimi. The lectin receptor protein isolated from brush border membrane vesicle of insect gut was purified to determine the mechanism of lectin binding to the gut. Purified receptor was identified as an endosymbiotic chaperonin, symbionin, using liquid chromatography-tandem mass spectrometry. Symbionin from endosymbionts of other aphid species have been reported to play a significant role in virus transmission by binding to the read-through domain of the viral coat protein. To understand the molecular interactions of the said lectin and this unique symbionin molecule, the model structures of both molecules were generated using the Modeller program. The interaction was confirmed through docking of the two molecules forming a complex. A surface accessibility test of these molecules demonstrated a significant reduction in the accessibility of the complex molecule compared with that of the free symbionin molecule. This reduction in surface accessibility may have an effect on other molecular interactive processes, including "symbionin virion recognition", which is essential for such symbionin-mediated virus transmission. Thus, garlic leaf lectin provides an important component of a crop management program by controlling, on one hand, aphid attack and on the other hand, symbionin-mediated luteovirus transmission.     

CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO

We have implemented in TOM/FRODO a protein crystallographic symmetry display and handling package, called CRYStallize. This package is designed as an aid in solving protein structures by molecular replacement methods. It allows the rotation/translation solutions provided by molecular replacement programs to be checked in a fast and easy way. Using CRYStallize, approximate solutions can also be improved by manual modifications. Symmetry-related objects, represented as surfaces, can be generated and handled in the same way as the reference molecules, thus permitting an efficient analysis of crystal packing and site accessibility. This program is available in the TOM/FRODO software release, which runs on the Silicon-Graphics workstations.     

Computer simulated modeling of biomolecular systems.

This paper describes the algorithm of a program used to simulate three dimensional models of molecules. In addition to open ended molecules the program also enables simulation of structures with constraints in the form of cyclic regions or fixed location of particular atoms. Several molecules can be handled in a single run and each molecule can have any number of contraints. Further, any number of conformations can be obtained for each constrained region. The program can be used for research in several areas of molecular biology, e.g., structure determination, conformational analysis and topographic comparisons.     

The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.     

Buried waters and internal cavities in monomeric proteins

We have analyzed the buried water molecules and internal cavities in a set of 75 high-resolution, nonhomologous, monomeric protein structures. The number of hydrogen bonds formed between each water molecule and the protein varies from 0 to 4, with 3 being most common. Nearly half of the water molecules are found in pairs or larger clusters. Approximately 90% are shown to be associated with large cavities within the protein, as determined by a novel program, PRO_ACT. The total volume of a protein's large cavities is proportional to its molecular weight and is not dependent on structural class. The largest cavities in proteins are generally elongated rather than globular. There are many more empty cavities than hydrated cavities. The likelihood of a cavity being occupied by a water molecule increases with cavity size and the number of available hydrogen bond partners, with each additional partner typically stabilizing the occupied state by 0.6 kcal/mol.     

Identification of Potential Inhibitors of H5N1 Influenza A Virus Neuraminidase by Ligand-Based Virtual Screening Approach

The neuraminidase (NA) of the influenza virus is the target of antiviral drug, oseltamivir. Recently, cases were reported that influenza virus becoming resistant to oseltamivir, necessitating the development of new long-acting antiviral compounds. In this report, a novel class of lead molecule with potential NA inhibitory activity was identified using a combination of virtual screening (VS), molecular docking, and molecular dynamic approach. The PubChem database was used to perform the VS analysis by employing oseltamivir as query. Subsequently, the data reduction was carried out by employing molecular docking study. Furthermore, the screened lead molecules were analyzed with respect to the Lipinski rule of five, drug-likeness, toxicity profiles, and other physico-chemical properties of drugs by suitable software program. Final screening was carried out by normal mode analysis and molecular dynamic simulation approach. The result indicates that CID 25145634, deuterium-enriched oseltamivir, become a promising lead compound and be effective in treating oseltamivir sensitive as well as resistant influenza virus strains.     

Cyclic adenosine 3',5'-monophosphate binding protein in developing myxospores of Myxococcus xanthus

The interaction of cyclic adenosine 3',5'-monophosphate (cAMP) with specific protein molecules was examined in the high-speed supernatant fraction of extracts made at stages throughout glycerol-induced myxospore development in Myxococcus xanthus. Experiments using 8-azido[32P]cAMP, a photoaffinity analogue of cAMP, and SDS - polyacrylamide gel electrophoresis showed that the nucleotide interacts with only a single protein band of 12 500 molecular weight. Both the identiy and amount of this protein remained constant throughout development. The binding protein was specific for cAMP; other nucleotides did not compete with cAMP for binding sites. A Scatchard analysis showed evidence of only a single class of binding sites with a high affinity for cAMP.     

SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small‐angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.