Chemical Computing Group Inc

Montréal, Canada

Chemical Computing Group Inc

Montréal, Canada
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Bio Simulation Technology Market is estimated at $1.01 billion in 2015 and is projected to reach $2.99 billion by 2022 growing at a CAGR of 16.6% from 2015 to 2022. Reduction in the cost of drug discovery and development and risk of failure of drug molecule are some of the factors driving the market growth. Furthermore, R&D investments in biotechnology and pharmaceutical industries, growth in the biologics and biosimilars markets, increased use of personalized medicines, technological advancements and periodic product upgradation are the key factors vitalizing the market growth. However, lack of standardization, high R&D costs associated with development of biosimulation software and lack of skilled professionals are some of the major restraints hampering the market growth. Industrial bioprocessing, nutraceuticals, agri-food production and biosimulation in the defense will provide opportunities for market growth over the forecast period. Pharmaceutical and biotechnology companies segment is valued to account largest share across the global market. North America is anticipated to command the largest share and Europe is expected to register the highest growth due to increasing government funding and the large number of pharmaceuticals and biotechnology companies in this region. Some of the key players in this market include Certara USA Inc., Simulation Plus Inc., Dassault Systèmes SA, Schrödinger Inc., Advanced Chemistry Development Inc., Chemical Computing Group Inc., Entelos Holding Corporation, Genedata Ag, Physiomics PLC, Rhenovia Pharma Ltd., Insilico biosciences, Archimedes, Insilico biotechnology, Accelrys, LeadScope and Compugen. Application Covered:  • Application In Drug Development  o Clinical Trials  o Preclinical Testing  • In Patient Validation  • Application In Drug Discovery  o Target Validation  o Target Identification  o Lead Identification/Discovery  o Lead Optimization Product Covered:  • Software  o Toxicity Prediction Software  o Molecular Modeling and Simulation Software  o Trial Design Software  o PK/PD Modeling and Simulation Software  o Pbpk Modeling and Simulation Software  o Other Software  • Services  o External/Contract Services  o In-House Services Regions Covered:  • North America  o US  o Canada  o Mexico  • Europe  o Germany  o France  o Italy  o UK  o Spain  o Rest of Europe  • Asia Pacific  o Japan  o China  o India  o Australia  o New Zealand  o Rest of Asia Pacific  • Rest of the World  o Middle East  o Brazil  o Argentina  o South Africa  o Egypt What our report offers:  - Market share assessments for the regional and country level segments  - Market share analysis of the top industry players  - Strategic recommendations for the new entrants  - Market forecasts for a minimum of 7 years of all the mentioned segments, sub segments and the regional markets  - Market Trends (Drivers, Constraints, Opportunities, Threats, Challenges, Investment Opportunities, and recommendations)  - Strategic recommendations in key business segments based on the market estimations  - Competitive landscaping mapping the key common trends  - Company profiling with detailed strategies, financials, and recent developments  - Supply chain trends mapping the latest technological advancements About Us Wise Guy Reports is part of the Wise Guy Consultants Pvt. Ltd. and offers premium progressive statistical surveying, market research reports, analysis & forecast data for industries and governments around the globe. Wise Guy Reports understand how essential statistical surveying information is for your organization or association. Therefore, we have associated with the top publishers and research firms all specialized in specific domains, ensuring you will receive the most reliable and up to date research data available.

Truchon J.-F.,Chemical Computing Group Inc. | Truchon J.-F.,Vertex Pharmaceuticals | Pettitt B.M.,University of Texas Medical Branch | Labute P.,Chemical Computing Group Inc.
Journal of Chemical Theory and Computation | Year: 2014

We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys. 1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. © 2014 American Chemical Society.

Clark A.M.,Chemical Computing Group Inc.
Journal of Chemical Information and Modeling | Year: 2010

Drug discovery projects often involve organizing compounds in the form of a hierarchical tree, where each node is a substructure fragment shared by all of its descendent nodes. A method is described for producing 2D depiction layout coordinates for each of the nodes in such a tree, ensuring that common fragments within molecular structures are drawn in an identical way, and arranged with a consistent orientation. This is achieved by first deriving a common numbering scheme for common fragments, then using this scheme to redepict each of the molecules, one fragment at a time, so that common fragments have common depiction motifs. Once complete, the distinct root branches can be overlaid onto each other, after which all of the fragments and whole molecules have a common layout and orientation. Several methods are described for preparing visual representations of molecular structure hierarchies alongside activity information. Combining high level tree display and structure depiction showing common features readily facilitates insight into structure-activity relationships. © 2010 American Chemical Society.

Maier J.K.X.,Chemical Computing Group Inc. | Labute P.,Chemical Computing Group Inc.
Proteins: Structure, Function and Bioinformatics | Year: 2014

The success of antibody-based drugs has led to an increased demand for predictive computational tools to assist antibody engineering efforts surrounding the six hypervariable loop regions making up the antigen binding site. Accurate computational modeling of isolated protein loop regions can be quite difficult; consequently, modeling an antigen binding site that includes six loops is particularly challenging. In this work, we present a method for automatic modeling of the FV region of an immunoglobulin based upon the use of a precompiled antibody x-ray structure database, which serves as a source of framework and hypervariable region structural templates that are grafted together. We applied this method (on common desktop hardware) to the Second Antibody Modeling Assessment (AMA-II) target structures as well as an experimental specialized CDR-H3 loop modeling method. The results of the computational structure predictions will be presented and discussed. © 2014 The Authors. Proteins published by Wiley Periodicals, Inc.

Tomberg A.,McGill University | Pottel J.,McGill University | Liu Z.,McGill University | Labute P.,Chemical Computing Group Inc. | Moitessier N.,McGill University
Angewandte Chemie - International Edition | Year: 2015

Adverse drug reactions are commonly the result of cytochrome P450 enzymes (CYPs) converting the drugs into reactive metabolites. Thus, information about the CYP bioactivation of drugs would not only provide insight into metabolic stability, but also into the potential toxicity. For example, oxidation of phenyl rings may lead to either toxic epoxides or safer phenols. Herein, we demonstrate that the potential to form reactive metabolites is encoded primarily in the properties of the molecule to be oxidized. While the enzyme positions the molecule inside the binding pocket (selects the site of metabolism), the subsequent reaction is only dependent on the substrate itself. To test this hypothesis, we used this observation as a predictor of drug inherent toxicity. This approach was used to successfully identify the formation of reactive metabolites in over 100 drug molecules. These results provide a new perspective on the impact of functional groups on aromatic oxidation of drugs and their effects on toxicity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Feldman H.J.,Chemical Computing Group Inc. | Labute P.,Chemical Computing Group Inc.
Journal of Chemical Information and Modeling | Year: 2010

A novel method for measuring protein pocket similarity was devised, using only the α carbon positions of the pocket residues. Pockets were compared pairwise using an exhaustive three-dimensional Cα common subset search, grouping residues by physicochemical properties. At least five Cα matches were required for each hit, and distances between corresponding points were fit to an Extreme Value Distribution resulting in a probabilistic score or likelihood for any given superposition. A set of 85 structures from 13 diverse protein families was clustered based on binding sites alone, using this score. It was also successfully used to cluster 25 kinases into a number of subfamilies. Using a test kinase query to retrieve other kinase pockets, it was found that a s?ecificity of 99.2% and sensitivity of 97.5% could be achieved using an appropriate cutoff score. The search itself took from 2 to 10 min on a single 3.4 GHz CPU to search the entire Protein Data Bank (133 800 pockets), depending on the number of hits returned. © 2010 American Chemical Society.

Chan S.L.,Chemical Computing Group Inc. | Labute P.,Chemical Computing Group Inc.
Journal of Chemical Information and Modeling | Year: 2010

A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed. This function is based on atoms and hydrogen-bond projected features. The concept is simply that atoms and features of a similar type (hydrogen-bond acceptors/donors and hydrophobic) tend to occupy the same space in a binding pocket and atoms of incompatible types often tend to avoid the same space. Comparison with some recently published results of small molecule alignments shows that the current scoring function can lead to performance better than those of several existing methods. © 2010 American Chemical Society.

Labute P.,Chemical Computing Group Inc.
Journal of Chemical Information and Modeling | Year: 2010

We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks. © 2010 American Chemical Society.

Larroque-Lombard A.-L.,McGill University | Larroque-Lombard A.-L.,Chemical Computing Group Inc. | Todorova M.,McGill University | Todorova M.,Chemical Computing Group Inc. | And 3 more authors.
Journal of Medicinal Chemistry | Year: 2010

Here, we report on the first synthesis of fluorescent-labeled epidermal growth factor receptor-DNA targeting combi-molecules, and we studied the influence of P-glycoprotein status of human sarcoma MES-SA cells on their growth inhibitory effect and cellular uptake. The results showed that 6, bearing a longer spacer between the quinazoline ring and the dansyl group, was more stable and more cytotoxic than 4. In contrast to the latter, it induced significant levels of DNA damage in human tumor cells. Moreover, in contrast to doxorubicin, a drug known to be actively effluxed by P-gp, the more stable combi-molecule 6 induced almost identical levels of drug uptake and DNA damage in P-gp-proficient and -deficient cells. Likewise, in contrast to doxorubicin, 4 and 6 exerted equal levels of antiproliferative activity against the two cell types. The results in toto suggest that despite their size, the antiproliferative effects of 4 and 6 were independent of P-gp status of the cells. © 2010 American Chemical Society.

Korb O.,University of Konstanz | Korb O.,Cambridge Crystallographic Data Center | Ten Brink T.,University of Konstanz | Raj F.R.D.V.P.,University of Konstanz | And 2 more authors.
Journal of Computer-Aided Molecular Design | Year: 2012

Due to the large number of different docking programs and scoring functions available, researchers are faced with the problem of selecting the most suitable one when starting a structure-based drug discovery project. To guide the decision process, several studies comparing different docking and scoring approaches have been published. In the context of comparing scoring function performance, it is common practice to use a predefined, computer-generated set of ligand poses (decoys) and to reevaluate their score using the set of scoring functions to be compared. But are predefined decoy sets able to unambiguously evaluate and rank different scoring functions with respect to pose prediction performance? This question arose when the pose prediction performance of our piecewise linear potential derived scoring functions (Korb et al. in J Chem Inf Model 49:84-96, 2009) was assessed on a standard decoy set (Cheng et al. in J Chem Inf Model 49:1079-1093, 2009). While they showed excellent pose identification performance when they were used for rescoring of the predefined decoy conformations, a pronounced degradation in performance could be observed when they were directly applied in docking calculations using the same test set. This implies that on a discrete set of ligand poses only the rescoring performance can be evaluated. For comparing the pose prediction performance in a more rigorous manner, the search space of each scoring function has to be sampled extensively as done in the docking calculations performed here. We were able to identify relative strengths and weaknesses of three scoring functions (ChemPLP, GoldScore, and Astex Statistical Potential) by analyzing the performance for subsets of the complexes grouped by different properties of the active site. However, reasons for the overall poor performance of all three functions on this test set compared to other test sets of similar size could not be identified. © Springer Science+Business Media B.V. 2012.

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