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Apuntes artculos

Combined 3D-QSAR modeling and molecular docking study on 1,4-dihydroindeno[1,2-c]pyrazoles as VEGFR-2 kinase inhibitors
Huahui Zeng, Huabei Zhang
The powerful genetic algorithm method implemented in the program AutoDock4.0 [59] was employed. All water molecules and its ligand were removed from the original Protein Data Bank file. Polar hydrogen atomswere added and Kollman charges. checked. For docking calculations, Gasteiger partial charges [52] were assigned to the 1,4-dihydroindeno[1,2c]pyrazoles derivatives and AAZ, and non-polar hydrogen atoms were merged.Each grid was centered at the crystal structure of the corresponding inhibitors. The grid dimensions were 4545453 with points separated by 0.375 . For all ligands, random starting positions, random orientations and torsions were used. The translation, quaternion and torsion steps were taken from default values in AutoDock. The Lamarckian genetic algorithmand the pseudo-Solis and Wets methods were applied for minimization using default parameters. The number of docking runs was 50. The population in the genetic algorithm was 50, the energy evaluations were 250 000 and the maximum number of iterations 27 000.

Molecular docking/dynamics studies of Aurora A kinase inhibitors


Tanaji T. Talele a,*, Mark L. McLaughlin b,c,
Molecular dynamic (MD) simulations MD simulations were carried out on energy-minimized Aurora A kinase-representative inhibitor docked whole complex using Impact 4.0 (Schrodinger, LLC) with the OPLS-AA force field and a generalized Born/solvent-accessible surface area (GB/SA) implicit water solvent model with a dielectric constant of 78. The complex was subjected to 1000 ps MD simulations at 300 K with an integration step of 1 fs and NVT as an ensemble type. All covalent bonds containing the hydrogen atoms were constrained using SHAKE algorithm, with a tolerance of 10_7 A . System coordinates were saved every 2 ps for further analysis. Three-dimensional structures and trajectories were visually inspected using the Maestro graphical interface. Root mean square (rms) deviations from the initial structures were calculated using superposition option in Maestro. An average structure obtained from the last 500 ps of MD simulations was refined by means of 1000 steps of steepest descent followed by conjugate gradient energy minimization. Conjugate gradient energy minimizations were performed four times using the positional restraints to all heavy atoms with 1000, 500, 100 and 0 kJ/mol A 2 force constants in sequence. The maximum number of cycles of minimization was 5000 and the convergence criterion for the energy gradient was 0.001 kJ/mol A . For the identification of hydrogen bonds, distance (H_ _ _A) cutoff of about 2.5 A and angle (DHA) >120 were used. Thus a strong hydrogen bond should have an H_ _ _A distance of about 2.5 A and DH A angle of >120

Identification of critical chemical features for Aurora kinase-B inhibitors using Hip-Hop, virtual screening and molecular docking
Sugunadevi Sakkiah, Sundarapandian Thangapandian, Shalini John, Keun Woo Lee
Refinement of homology model using molecular dynamics simulation Molecular dynamics (MD) simulation was performed to refine the side chain orientations and also to gain a better relaxation as well as more correct arrangement of the atoms in Aurora kinase- B model. The GROningen MAchine for Chemical Simulations (GROMACS) V3.3 package [27,28] was used

to solvate a model in a cubic box of dimension 1 nm by applying GROMACS force field [29]. The SPC water model was used in order to create the aqueous environment. Particles mesh Ewald (PME) [30] electrostatic and periodic boundary conditions were applied in all directions. The system was neutralized by adding eight Cl_ counter ions by replacing eight water molecules. It was subjected to a steepest descent energy minimization until a tolerance of 1000 kJ/mol reached, therefore the system can be get rid of the high energy interactions and steric clashes. All the bond lengths were constrained with [31] the LINCS [21] method the energy minimized system was treated for 100 ps equilibration run. The pre-equilibrated system was consequently subjected to 5 ns production MD simulation, with a time-step of 2 fs at constant temperature (300 K), pressure (1 atm) and without any position restraints [32]. Snapshots were collected every 5 ps and all the analyses of the MD simulation were carried out by GROMACS analysis tools. From the 5 ns MD simulation, average structure with low RMSD value was selected as the best model for molecular docking studies.

Role of Arg301 in substrate orientation and catalysis in subsite 2 of Dalanine: D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: A molecular docking study
Francis C. Neuhaus
The docked energy is the sum of the intermolecular and the internal energies. For a representative docking instance, the orientation or pose with the lowest estimated free energy (DG) of binding (docked energy + torsional free energy _ unbound systems free energy) was chosen in each cluster.

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases


Claudio N. Cavasotto* and Ruben A. Abagyan
Induced molecular flexibility is fundamental to understanding the principles of molecular recognition between ligand and receptor. Upon ligand binding, many systems undergo rearrangements, which range from local motions of side-chains to large domain movements. In any case, receptor flexibility might have a dramatic impact in the ligand docking problem and VS. It has been shown that even small changes in the receptor conformation can be important in computing binding affinities.6 The importance of receptor flexibility and its implication in drug discovery has been highlighted in two excellent reviews in this field, 7,8 and everything points in the direction that protein mobility will have an increasing role in computeraided drug design in the future. Dealing with protein flexibility is essential to predict the orientation and interactions of a ligand within a binding pocket in the absence of experimental structural information

Molecular modeling of the heterodimer of human CFTRs nucleotide-binding domains using a proteinprotein docking approach
Sheng-You Huang, Diana Bolser, Hao-Yang Liu, Tzyh-Chang Hwang, Xiaoqin Zou
Construct human NBD1NBD2 heterodimer by proteinprotein docking Instead of using the conventional superimposition method described in Section 1, we proposed to use a proteinprotein docking approach for model construction. We performed two types of docking calculations with ATP-free and ATP-bound NBD monomeric structures. In both cases, we obtained the biologically correct NBD1NBD2 heterodimeric structures. Considering the critical role of ATP molecules in NBD1NBD2 dimerization [24], we focused on the docking study with ATPbound NBD monomeric structures. Specifically, NBD1 and NBD2 monomers were treated as two different proteins. The ZDOCK (version 2.1) proteinprotein docking program [27] was used to search globally all possible binding configurations between NBD1 and NBD2. During protein protein docking with human NBDs, the default parameters of ZDOCK were used.

Namely, NBD1 was fixed and NBD2 was uniformly sampled with an Euler angle interval of 15_ in the entire rotational space, yielding a total of 3600 rotations. For each rotation of NBD2, the complete search over the translational space was performed by the Fast Fourier Translational (FFT) algorithm with a grid spacing of 1.2A , and only the top translation of NBD2 with the best shape complementarity according to the scoring function in ZDOCK was kept. This yielded a total of 3600 putative NBD1NBD2 binding modes in a global search. By default, the top Fig. 1. 2000 putative NBD1NBD2 binding configurations were retained in the ZDOCK final results. These 2000 NBD1NBD2 binding configurations from ZDOCK were further refined and rescored using a more accurate scoring function, ITScore-PP, recently developed in our group [28]. The top NBD1NBD2 binding mode that has the lowest ITScore-PP score was chosen. This predicted structure was then optimized via AMBER force field minimization. The optimized NBD1NBD2 structure was used as the protein target for docking ATP and genistein. It should be noted that the C-terminal extension of NBD1 into the R domain (i.e., the last 31 residues at the C-terminus) was not included in our modeling study for two reasons. First, this segment was found to exhibit prominent flexibility in crystallographic studies [9,11]. Second, our functional studies with DR-CFTR suggest that a deletion of the R domain has little effect on CFTR gating [2932]. It should also be noted that residues 412428 were missing in the crystal structure (1XMI) and therefore were not included in the present modeling study.

Role of the omega loop in specificity determination in subsite 2 of the d-alanine:D-alanine (d-lactate) ligase from Leuconostoc mesenteroides: A molecular docking study
Francis C. Neuhaus
AutoDock 4.2 uses a grid-based algorithm and not a trajectory based program to evaluate trial conformations, docking can occur on either surface receptor sites or in internal cavity sites of the protein. The grid size for the search space was set at 464646 centered in the subsite 2 cavity with a default grid point spacing of 0.375A .

Insights into the structural and conformational requirements of polybrominated diphenyl ethers and metabolites as potential estrogens based on molecular docking
Weihua Yang a,b, Si Wei a, Hongling Liu a, Hongxia Yu
Docking reliability Prior to identifying potential xenoestrogens, the computational procedure was validated by applying it to ligands for which ERa-ligand complexes are crystallographically determined. For each of these complexes, the ligand was extracted and then redocked into the ERa binding site using the Surflex-Dock docking package. Surflex- Dock generated ligand poses close to the X-ray conformation more often than the other docking programs (Cross et al., 2009). The accuracy of this computational approach in reproducing the crystallographically detected conformation was estimated on the basis of the heavy atoms rootmean-square-deviation (RMSD) between the ligand coordinates in the docking pose and in the crystal structure. A lower RMSD value indicates a good docking. RMSD value that is smaller than 2.0 is considered acceptable, i.e., the predicted binding modes reproduced very well the crystallographically determined ligand conformation. The average value of RMSD values between the 20 docking poses and its original X-ray structure position is 0.35 , 0.16 and 1.29 , respectively, for DES, E2 and GEN. Among the calculated RMSD values, none was higher than 2.0 , suggesting that a high docking reliability of Surflex-Dock in reproducing the experimentally observed binding mode for estrogen receptor agonists, and the parameter set for the Surflex-Dock simulation is reasonable to reproduce the X-ray structure.

Prediction of MEF2ADNA interface by rigid body docking: A tool for fast estimation of protein mutational effects on DNA binding
Francesca Fanelli a,b,, Stefano Ferrari
The proteinprotein docking algorithm ZDOCK has been challenged for the first time to predict proteinDNA contacts. The computational approach defined in this study has proven effectiveness in fast in silico estimations of mutational effects of the MEF2A transcription factor on DNA binding. The rigid-body docking algorithm, ZDOCK, proved high effectiveness in predicting proteinprotein complexes (Chen et al., 2003; Chen and Weng, 2003). The excellent performance of the program is essentially due to its scoring function, which properly takes into account the major determinants of proteinprotein association, i.e., shape and electrostatic complementarities, as well as desolvation. Moreover, the Fast Fourier transform algorithm employed by the program makes the search extremely fast and exhaustive
Chen, R., Li, L., Weng, Z., 2003. ZDOCK: an initial-stage protein-docking algorithm. Proteins 52, 8087. Chen, R., Weng, Z., 2003. A novel shape complementarity scoring function for proteinprotein docking. Proteins 51, 397408.

Rigid-body docking simulations were carried out by means of ZDOCK 2.3 (Chen et al., 2003; Chen and Weng, 2003). Since ZDOCK has been made to predict the interaction interface in proteinprotein complexes, in this study, it was ad hoc parametrized for DNA, by adding the missing atomic radii, atomic contact energies (ACE) (Zhang et al., 1997) and CHARMM22 atomic charges (MacKerell et al., 1998). The novel parameters for the DNA nucleotides are available as supplementary material. The DNA fragment was kept fixed (i.e., target), whereas the protein MEF2A, in its wild type or mutated forms, was allowed to rotate and translate around the target (i.e., probe). A 128*128*128 point grid with a spacing of 1.2 was employed. A rotational sampling interval of 6 was used, i.e., dense sampling, and the best 4000 solutions were retained and ranked according to the ZDOCK score (i.e., the default number of solutions provided by the program is 2000).

Complex-type-dependent scoring functions in proteinprotein docking


Chun Hua Li a,1, Xiao Hui Ma a,b,1, Long Zhu Shen a, Shan Chang a, Wei Zu Chen a, Cun Xin Wang
Docking algorithms have progressed in recent years, which can dock unbound (separately crystallized) proteins to obtain the structure of the complex with small structural changes accompanying complexation [5 19]. The accuracy and reliability of docking algorithms still need to be assessed if they are to become widely used. This depends on docking algorithms with an efficient procedure to generate potential structures and a good scoring function to distinguish the near-native structures from a large number of non-native ones. The known scoring functions include surface complementarity (SC) [5,6], surface complementarity together with an electrostatic filter [20,21], knowledge-based statistical potential such as atomic contact energy (ACE) [22], the residue pair potential (RP) [23] and DFIRE [24]

Study of microheterogeneous environment of protein Human Serum Albumin by an extrinsic fluorescent reporter: A spectroscopic study in combination with Molecular Docking and Molecular Dynamics Simulation (analisis de estabilidad MD)
Sankar Jana, Sasanka Dalapati, Shalini Ghosh, Nikhil Guchhait

Molecular docking simulations Molecular docking was performed to obtain the protein-ligand binding energy and to identify the potential ligand binding sites. The blind docking experiments were performed with the help of AutoDock4.2 [40] and AutoDockTools (ADT) software using the Lamarkian Genetic Algorithm (LGA) based on the adaptive local method search. The energy based Autodock scoring function includes terms accounting for short range van der Waals and electrostatic interactions, the loss of entropy upon ligand binding, hydrogen bonding and solvation. For the recognization of the binding sites in HSA, docking was carried out with setting of grid box size 120 x 90 x 126 along x, y, z axes covering the whole protein with a grid spacing 0.502 [13] after assigning the protein and probe with the Kollman charges. The grid center was set at 29.45, 31.82, 23.48. Initially, AutoGrid was run to generate the grid map of various atoms of the ligand and receptor. After the completion of grid map, ligand flexible docking simulations were performed with 200 runs and 2.5 x 106 energy evaluations, 27000 numbers of generations, 300 GA population and root mean square cluster tolerance 2.0 [15] per run. Among 200 runs 10 minimum energy conformers were chosen according to ranking and scoring [12, 15]. Finally the lowest energy conformation was used for docking analysis with the help of PyMOL 0.99rc6. MD Simulation of HSA and HSA-DMAPPDA complex The MD simulations of these two systems were performed in three stages. In the first stage, 5000 steps energy minimization of the total system were carried out at 298K temperature. The 2nd stage was a 100ps NPT dynamics using the Langevin piston pressure control at 310K and 1.01325 bar. The Langevin damping coefficient and piston decay was set as 5ps-1 and 50fs, The final stage was a 4ns NVT simulation. Periodic boundary conditions and the Particle-mesh Ewald method [44] were applied for a complete electrostatic calculation. Simulation was carried out with an integration time step of 2fs using SETTLE algorithm, while keeping all bonds to hydrogen atoms rigid. The trajectory was stored every 2ps and further analyzed with the VMD 1.8.7. software and tcl script for root mean square deviations (RMSD) [16, 45] and radius of gyration (Rg). For HSA, the data point fluctuations are 0.730.03 nm where as for the complex they are 0.600.02 nm [45]. The decrease in RMSD value of the complex from that of the free HSA indicates conformational change, increased rigidity and stability of the protein upon binding with ligand

Binding interaction between plasma protein bovine serum albumin and flexible charge transfer fluorophore: A spectroscopic study in combination with molecular docking and molecular dynamics simulation

(analisis de

estabilidad MD)
Sankar Jana, Sasanka Dalapati, Shalini Ghosh, Nikhil Guchhait

Dissecting substrate specicity of two rice BADH isoforms: Enzyme kinetics, docking and molecular dynamics simulation studies

(analisis de

estabilidad MD)
Kultida Jiamsomboon , Witcha Treesuwan, Nonlawat Boonyala
Molecular docking analysis on Autodock 4.0 [20]. For docking ligand, the rotational bonds of the side chain were treated as flexible whereas those of main chain were regarded as rigid. Grid boxes were created to cover the substrate-binding domain of the protein. The size of the grid box was set at 60 _ 60 _ 60 3 and the center of the grid boxwas set at 7.545 (x), 3.238 (y), and 33.596 (z). The Lamarckian Genetic Algorithm (LGA) with 100 runs was used as the search algorithm. The population size was set at 150. Three-dimensional structures of OsBADHseBet-ald or OsBADHseGAB-ald with the lowest energy and highest populations were visualized and analyzed by PyMOL [19] and Discovery Studio 2.5. Molecular dynamics simulations The selected models of OsBADHseBet-ald or OsBADHseGAB-ald complexes obtained from docking were used for MD simulations. MD simulations were performed using the AMBER10 simulation package with the Cornell force field [21]. OsBADH1 and OsBADH2 contained 505 and 503 amino acid residues, respectively. All complexes were immersed in an octahedral box of TIP3P water [22] with the distance between solute surface and the edge of the box set at 10 . Minimization was achieved stepwise as follows: 2000 steps for hydrogen atoms, 2000 steps for solvent water molecules and 5000 steps for all atoms in the system. The equilibration was perfomed in the carononical ensemble (NVE) at 300 K; during the initial 100 ps all atoms in the protein were restrained while in the following 100 ps all atoms were set free. MD simulations were carried out under an isobariceisothermal ensemble (NPT), at 1 atm and 300 K. Equilibration was achieved when the system was stable and this was followed by a production phase which was harvested during the last 500 ps of the trajectory. Root-mean-square displacement (RMSD) values for distances between interacting amino acid residues, hydrogen bonds and binding free energies were also calculated. Structural and dynamic studies of both OsBADHs with aldehyde substrates were carried out by MD simulations. The OsBADH complex comprised OsBADHs, NAD, and their aldehyde substrates. The trajectories for four simulation systems: OsBADH1eBetNAD, OsBADH1eGAB-NAD, OsBADH2eBet- NAD and OsBADH2eGAB-NAD, were analyzed over the last 500 ps after reaching equilibrium. RMSD fluctuations for OsBADH complexes were monitored to determine the structural equilibrium (Supplementary data Fig. S3). Overall, the results confirmed that all components were well in equilibration throughout the analysis range thus allowing us to determine binding energies and preferred binding sites for each complex. Thermodynamic parameters for OsBADHseBet-ald and OsBADHseGAB-ald complexes are presented in Table 5. The energy component involved in binding indicated that the simulation models could be separated into two sets based on the ligand driving force for the interaction. Set I was the binding of OsBADHs to Bet-ald. The important interactions for these models were electrostatic interactions (DEELE), which played a major role as the main attractive force. The van der Waal interactions in the gas phase (DEVDW) were the second most important energy component for this binding. Set II contained models of OsBADHs binding to GAB-ald in which, unlike OsBADHseBet-ald, the electrostatic interaction was not the main interaction. Electrostatic interactions for OsBADH1 and OsBADH2 were _22.62 and _22.67 kcal/mol, respectively, while the van der Waal interaction was _17.74 kcal/ mol for OsBADH1 and _19.05 kcal/mol for OsBADH2. It is noted that the nonpolar interaction of solvation (DDGSA) of the four complexes was lower than the van derWaal interaction in gas phase (DEVDW). This may be caused by hydrogen bonding interactions during complex formation, resulting in the reduction of the polar surface exposed to water solvent. Additionally, the unfavorable energy component might have resulted from the electrostatic contributions of solvation (DDGPB), which are 246.01, 24.66, 227.09 and 28.64 kcal/mol for OsBADH1eBet-ald, OsBADH1eGAB-ald, OsBADH2eBet-ald and OsBADH2eGAB-ald, respectively. According to the total binding energy of OsBADH1eligand complexes, GAB-ald was represented as a higher potential ligand for OsBADH1 than Bet-ald with DDGMM/PBSA of _18.34 kcal/mol, which agreed well with the kinetic result. However, in contrast to the kinetic data the binding energy of OsBADH2eBet-ald (_17.65 kcal/mol) was stronger than OsBADH2eGAB-ald (_15.78 kcal/mol). To confirm our results, the simulation experiments were carried out in triplicate and the similar results were obtained. While the binding energy from docking in which the conformation of the enzyme was kept rigid correlated well with the kinetic results, MD simulations in which the enzyme and ligands were allow to be flexible revealed a slightly different binding energy. This suggested that the dynamics of OsBADHs and the aldehyde substrates significantly affected the binding event. Conformational changes of amino acid residues around the binding site of OsBADH2 are discussed in the next section. Unlike molecular docking, MD simulations allowed the proteineligand complex to be fully relaxed in the solvent environment, thereby generating more reliable binding properties. In the OsBADH1 system, the OsBADH1eGAB-ald complex showed the lowest binding energy from docking and exhibited the best binding from molecular dynamics simulation. However, in the OsBADH2 system, the OsBADH2eGAB-ald complex gave the lowest binding energy from docking but not from MD simulations. In order to understand this difference, hydrogen bonding interactions and MMGBSA decomposition of the binding energy were considered.

Exploring the molecular basis of the enantioselective binding of penicillin G acylase towards a series of 2-aryloxyalkanoic acids: A docking and molecular dynamics study
Antonio Lavecchia a,*, Sandro Cosconati a, Ettore Novellino a, Enrica Calleri b, Caterina Temporini b, Gabriella Massolini b, Giuseppe Carbonara c, Giuseppe Fracchiolla c, Fulvio Loiodice
Molecular dynamics simulations When predicting the posing of a ligand into a protein, docking can provide a good starting point for further calculations with the aim of evaluating the stability of the predicted interactions involved in binding. In this respect, MD simulations were undertaken to consider the effects of the receptor flexibility and the explicit water solvation on the complex of interest During the MD simulations all compounds remained in a stable binding position with low rmsd (root-mean square deviations) fluctuations, thus, confirming the feasibility of the binding poses predicted by AutoDock
free energy of binding = RT ln(10
pKd

).

Molecular docking study and development of an empirical binding free energy model for phosphodiesterase 4 inhibitors
Fernanda G. Oliveira,a Carlos M. R. SantAnna,b Ernesto R. Caffarena,c Laurent E. Dardenned and Eliezer J. Barreiro

Molecular dynamics The MD approach is a suitable computational technique to study the flexibility of macromolecules. To analyze the conformational stability and rigidity of the enzyme active site Docking implemented in the AutoDock program (version 3.0). A Lamarckian Genetic Algorithm 57 with an initial population size of 100 random individuals was used with probabilities of 0.02 and 0.8 for gene-mutation and crossover operators, respectively. The pseudo-Solis and Wets local search method was used with a probability of 0.06 to be applied on an individual in the population. The docking calculations were performed by using a grid map of 60 60 60 points centered in the enzyme active site, with 0.375 A grid-point spacing. The MMFF9458 partial atomic charge parameter set was used for all ligands. For each ligand we performed flexible ligand docking calculations using three different initial conformations (obtained by manual docking) each initial ligand conformation we performed 40 independent docking runs with a maximum number of 2.5 106 energy evaluations per run. Therefore, for each ligand we obtained 120 binding conformations, which were clustered by their root-mean-square positional deviation (rmsd)

Computational molecular docking assessment of hormone receptor adjuvant drugs: Breast cancer as an example
Sayan Mukherjee, Durjoy Majumder
Molecular docking For getting the drug-receptor binding energy procedures of molecular docking were followed. The detailing of the procedure is as follows. 1. Preparing the ligand and macromolecule files for AutoDock: The PDB files obtained from the World Wide Web repository are often far from perfect for docking study and present with potential problems like missing hydrogen atoms, multiple molecules, added waters and related problems. Using the GUI (graphic user interface) of ADT, we prepared the files as follows: (a) The Macromolecule file: The downloaded PDB files were first read in ADT, added waters removed and polar hydrogens were added. ADT then checked if the molecule had charges, if not ADT checked whether the molecule was a peptide (by checking whether all of its residues names appear in the standard set of 20 commonly occurring amino acids). If the molecule was found to be a peptide Kollman charges were added, else Gasteiger charges were added. Finally solvation parameters were added and the files saved with .pdbqs extension (where q and s represent charge and solvation, respectively). (b) The Ligand file: In a similar procedure, the ligand files were read in ADT, all hydrogens added, charges added and non-polar hydrogens merged and saved with .pdbqs extension.ADTthen automatically determined the best root. The root is defined as the fixed portion of the ligand from which rotatable branches sprout. Next, we defined rotatable bonds in the ligand, making all amide bonds non-rotatable and set the number of active torsions to fewest atoms. The ligand file was then saved with ligand.out.pdbq extension ( q representing charge). 2. Preparing the grid parameter file: For the calculation of docking interaction energy, a three-dimensional box (grid) was created in which the protein molecule is enclosed. The grid volume was large enough to allow the ligand to rotate freely, even with its most fully extended conformation. The parameters required to create such a grid were stored in the Grid Parameter File with molecule.gpf extension. 3. Then AutoGrid3 job was run; autogrid3 creates one map for every type of atom in the ligand. For example a molecule having C, N, O, H, maps will be created as molecule.C.map, molecule.N.map, molecule.O.map, molecule.H.map. These are grid maps in ASCII format for readability by AutoDock. AutoGrid also generates corresponding output of the macromolecular file with the extension molecule.glg. 4. Preparing the docking parameter file: The docking parameter file, which instructs AutoDock about the ligand to move, the map files to use, and other properties defined for the ligand was created. AutoDocks search methods include the Monte Carlo simulated annealing (SA) method, the Genetic Algorithm (GA), local search (LS) and the hybrid genetic algorithm with local search (GALS). The latter is also referred to as

the Lamarckian genetic algorithm (LGA) because offsprings are allowed to inherit the local search adaptations of their parents and this was the chosen algorithm for our analysis. 5. Finally, the AutoDock job was run from the GUI (graphical user interface) of ADT and the docked ligand files (.dlg extension) were used for study. The dlg files were read in ADT as well as in PyMol to calculate the binding energies in the docked ligandprotein complexes. The entire procedure is schematically shown in Fig. 1.

Modelling and Bioinformatics Analysis of the Dimeric Structure of House Dust Mite Allergens from Families 5 and 21: Der f 5 Could Dimerize as Der p 5
Souad Khemili1* Jean Marc Kwasigroch2 Tarik Hamadouche1 Dimitri Gilis
In this study, 30 runs for each protein and each template were carried out using MODELLER standard parameters. The quality of our models was assessed by two types of energy functions: a semi-empirical force field (Gromos) and a knowledge-based energy function (Anolea). Steepest descent energy minimizations of the 30 models of each allergen were performed using Gromacs3.3 (17) with the GROMOS96 45a3 force field. The Anolea score (18) was also computed for each model after energy minimization. Anolea is a knowledge-based energy function that evaluates the non-local environment (NLE) of each heavy atom in the model. The NLE is defined as the set of all heavy atoms within the distance of 7 that belong to amino acids farther than 11 residues along the sequence in the analyzed polypeptide.

Computational Methods for Predicting ProteinProtein Interactions


A. Walker-Taylor and D.T. Jones

Proteinprotein interactions perform an integral role in a diverse range of cellular and extracellular processes. These interactions provide a means for cells to communicate both internally and externally; they facilitate the anabolic and catabolic reactions of metabolism; they are important for transcriptional and translational control; and they are also important in maintaining cell structure. These examples are by no means exhaustive, however. Understanding these protein protein interactions is a very important area of research in light of their global implications. Moreover, the knowledge of how to predict these interactions would be extremely useful and could be exploited to block these interactions as a therapeutic intervention, for example, and also to implicate novel functional interactions. Finally, proteins may interact with other proteins. These interactions may provide a variety of functions such as catalytic, structural, localization, cleavage, transferral, or inhibitory functions

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking


Gwo-Yu Chuang,* Dima Kozakov,* Ryan Brenke, Stephen R. Comeau, and Sandor Vajda It is important to note that the problem of protein-protein docking substantially differs from that of docking small ligands to proteins. In protein-small molecule interactions, the binding pocket of the target is generally known, and due to the restricted nature of the problem and the small size of the ligand, the exibility of the latter usually can be taken into account. In contrast, in protein-protein docking information on the interaction site is rarely available, and in most cases it is necessary to explore all possible interactions, generating and evaluating billions of putative conformations of the complex. Due to this enormous search space, protein-protein docking generally starts with rigid body search, frequently using simplied protein models and simplied energy functions. The use of rigid protein models requires tolerating some levels of overlaps, and since the energy functions are approximate, the structures that are close to the native conformation do not necessarily have the lowest energies. Thus, to avoid losing potentially useful conformations it is necessary to retain a large number (usually 200020,000) of low energy docked structures for further processing. Thus, the initial docking yields a long list of candidate structures rather than a small number of models, and obtaining

meaningful results requires some form of postprocessing, which includes the renement of the docked conformations, usually accounting for some level of exibility (21). Over the last few years we have developed a multistage docking method that performs rigid body docking, retains a number of low energy conformations, clusters them using pairwise RMSD as the distance measure, and then ranks the clusters according to their size, i.e., identifying conformations that have many neighbors within a given clustering radius (11,22). The method is based on the observation that, in the free energy landscapes of partially solvated receptorligand complexes, the free energy attractor at the binding site generally has the greatest breadth among all local minima. It was shown that the optimal clustering radius is ;10 A in agreement with the maximum distance two proteins effectively interact in solution (22). Since the native state is identied by clustering, the goal of the rigid body docking is to generate a substantial number of near-native structures or hits within 10 A RMSD from the native state. Although 10 A RMSD may appear to be very broad, one has to keep in mind that the prime aim is nding the region of interest in the conformational space, and the structures in this region will be further rened by methods that account for the exibility of side chains and possibly for the exibility of some backbone regions