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2012.10.02 YTN 사이언스 "보다 정밀한 신약발굴 기술 개발"
조은성 대표 인터뷰
 

게시물 구독

Schrödinger Software Release 2018-2

게시자: Quantum Bio Solutions LLC, 2018. 6. 7. 오전 7:59   [ 2018. 6. 7. 오전 8:17에 업데이트됨 ]

새로운 Schrödinger Software Release 2018-2 버전을 아래 링크에서 다운로드 받으실 수 있습니다.

이번 새로운 버전에서는 제품 대부분에서의 성능 향상 및 새로운 기능이 추가되었습니다.

Schrödinger  의 아래 웹페이지에 small molecule membrane permeability, QSAR 모델, Materials Science 의 physical property 예측을 포함한 새로운 튜토리얼이 추가되었습니다.

2018-2 버전의 신규 특징은 아래 링크에서 확인하실 수 있습니다.

Schrödinger社, ONO약품과 연구협력 체결

게시자: Quantum Bio Solutions LLC, 2018. 1. 11. 오후 10:18   [ 2018. 1. 11. 오후 10:26에 업데이트됨 ]

"Schrödinger Announces Research Collaboration with Ono Pharmaceutical"


"오노, 美 슈뢰딩거와 신약표적 제휴"
독자적 컴퓨터 신약개발기술 활용해 저분자화합물 개발




Simulations Plus Finalizes Distributor Agreement With Quantum Bio Solutions

게시자: Quantum Bio Solutions LLC, 2017. 4. 10. 오전 3:09

퀀텀바이오솔루션즈는 제약, 생명공학 및 화학 산업에서 사용하는 모델링 및 시뮬레이션 솔루션(ADMET 특성 예측, PBPK 모델링 및 약리학)의 선두 업체인 Simulations Plus, Inc.의 판매 계약을 체결하였음을 알려 드립니다.

Simulations Plus, Inc. (Nasdaq: SLP), a leading provider of modeling & simulation solutions for the pharmaceutical, biotechnology, and chemicals industries, today announced that it has entered into a distributor agreement in South Korea with Quantum Bio Solutions (Q-Bio).

자세한 내용은 아래 링크를 참고하시기 바랍니다.
For more information, please refer to the link below.


Schrödinger Software 2016-1

게시자: Quantum Bio Solutions LLC, 2016. 2. 25. 오전 5:11


Schrödinger Software 2016-1 버전이 출시되었습니다. 
신규 기능은 다음과 같습니다.

Molecular Dynamics

Significant improvement in Metadynamics performance [ 2016-1 ]
U-series now used by default for long-range electrostatics replacing PME [ 2016-1 ]
User control of initial random seed for molecular dynamics calculations [ 2016-1 ]

FEP+

View ligand torsion profiles in FEP+ Edge analysis [ 2016-1 ]

Empirical and QM-based pKa Prediction

Improved speed and accuracy in Epik pKa prediction [ 2016-1 ]
- Predictions now 20-40% faster
- Improved pKa accuracy for standard benchmarks


Ligand Preparation and Conformation Generation

Improved speed of LigPrep [ 2016-1 ]
- Ligands now prepared 2-3 times faster from 2D or SMILES input
Refit MacroModel OPLS3 GB/SA parameters for water to improve solvation free energies [ 2016-1 ]

Ligand Docking

VSW now runs OPLS3 calculations by default for SP and XP Glide docking [ 2016-1 ]

Cheminformatics

New AutoQSAR product automatically creates QSAR models that can be validated and employed within Maestro [ 2016-1 ]
- Easily create predictive QSAR models automatically following best-practices methods [ 2016-1 ]
- Easily validate and employ QSAR models directly from Maestro [ 2016-1 ]
- Quickly and easily deploy QSAR models via LiveDesign or other cheminformatics platforms [ 2016-1 ]

Quantum Mechanics

Added two dispersion-corrected long-range corrected (LRC) functionals: CAM-B3LYP-D3 and wPBE-D3 [ 2016-1 ]
Optionally improve geometry optimization convergence by automatically switching from internal to cartesian coordinates (command-line only) [ 2016-1 ]
Print out phosophorescence rates at the end of ZORA-SO TDDFT calculations [ 2016-1 ]
Compute dipole and multipole moments with ZORA [ 2016-1 ]
Excited state frequency calculations using numerical TDDFT differentiation [ 2016-1 ]

Protein Preparation

Automatically recognize and return the most suitable ligand ionization/tautomeric state even when the ligand interacts with a metal ion [ 2016-1 ]
In the protein reliability report optionally display crystal mate clashes [ 2016-1 ]

Schrödinger Software 2015-4 출시

게시자: Quantum Bio Solutions LLC, 2015. 11. 12. 오후 6:33

Schrödinger Software 2015-4 버전이 출시되었습니다. 
신규 기능은 다음과 같습니다.

[Maestro Graphical Interface]

licensing과remote job submission의 새로운 인터페이스 [ 2015-4 ]
2D Sketcher에서 2D->3D 분자 구조 변환 속도 향상   [ 2015-4 ]
Automatic resolution setting for molecular surfaces [ 2015-4 ]
Structure drawing and measurements are now aware of Workspace periodicity [ 2015-4 ]


[Molecular Dynamics]

2x speedup on GPU with new GPU Desmond backend (v1.6) [ 2015-4 ]
Better energy conservation [ 2015-4 ]
Reduced memory requirements [ 2015-4 ]
Improved radial distribution function interface [ 2015-4 ]
     - Simplified atom selection
     - Backend jobs now runs under Jobcontrol
MD Analysis [ 2015-4 ]
     - Calculate order parameter; Supported in backend only


[FEP+]

Improvements from new GPU Desmond backend (v1.6) [ 2015-4 ]
     - 2x speedup on GPU with new GPU Desmond backend (v1.6)
     - Improved energy conservation
     - Reduced memory requirements enable single perturbation to be run on one GPU card instead of four cards as previously required
Easily perform methyl, halogen, and heterocycle scans from a lead compound to explore SAR and identify activity cliffs [ 2015-4 ]
Improved tools to diagnose unconverged perturbations in FEP Mapper Analysis [ 2015-4 ]


[Ligand Preparation and Conformation Generation]

기존 ConfGen보다 100배 이상 속도 향상된 새로운 ConfGen 알고리즘 [ 2015-4 ]
Macromodel 기반 macrocycle conformation보다 20배 이상 속도 향상된 Prime 프로그램 기반 새로운 macrocycle conformation generator [ 2015-4 ]


[Quantum Mechanics]

Zeroth Order Regular Approximation with spin-orbit coupling (ZORA-SO) is available [ 2015-4 ]
Singlet to triplet excitations and oscillator strengths can be computed with the ZORA-SO / TDDFT method [ 2015-4 ]
Optimize excited state geometries with the TDDFT method [ 2015-4 ]


[Workflows & Pipelining]

Includes the latest version of KNIME (v2.12.0) [ 2015-4 ]
Faster and more robust Extract mae atom/bond properties and Extract Maestro properties nodes [ 2015-4 ]
A configured reader node is added when dragging-and-dropping a Grid, Phase hypothesis file into the workspace [ 2015-4 ]
Molecule Reader - Add option to specify the output column name. URL supported and editable [ 2015-4 ]
Desmond molecular dynamic and Chemistry external tool nodes accept a trajectory as input [ 2015-4 ]

[Materials Science Suite]

Fluorescence/PL maximum now available as an optoelectronics property [ 2015-4 ]
Periodicity Toolbar Option to make a P1 cell from the workspace [ 2015-4 ]
Optoelectronics calculations can be run with parallel Jaguar jobs [ 2015-4 ]
Single and Multi Complex Builders can clean resulting structures [ 2015-4 ]
Polymer crosslink improvements: [ 2015-4 ]
Option to allow or disallow self-crosslinking
Longer simulation times allowed for equilibration
Many stability improvements
Better naming of output files
Analysis information output at each step
Optoelectronics, Electron Coupling and Bond Dissociation workflows can be restarted from a new Workflow Restart GUI [ 2015-4 ]
New option to fragment molecules when building slabs and interfaces [ 2015-4 ]
New Analysis stage option in Multistage MD Workflow panel [ 2015-4 ]
General improvements in speed and stability for operations on nano and periodic systems [ 2015-4 ]

Schrödinger Software Release 2015-3

게시자: Quantum Bio Solutions LLC, 2015. 8. 17. 오후 7:58   [ 2015. 8. 17. 오후 8:04에 업데이트됨 ]

Schrödinger Software 2015-3 버전이 출시되었습니다. 

간략한. 신규 기능은 다음과 같습니다.

[MAESTRO]

 - 신규 OPLS3 Force Field 도입
 - Force Field Builder
 - Shape Screening 속도 향상
 - 향상된 pKa 예측

[QUANTUM MECHANICS]

 - Added support for 13 long-range-corrected (LRC) DFT functionals.
 - Employ M08-HX and M08-SO DFT functionals.
 - Improved robustness of Intrinsic Reaction Coordinate (IRC) calculations.
 - Apply scalar relativistic zeroth-order regular approximation (ZORA) in single point calculations.

[MATERIALS SCIENCE SUITE]

 - New panel for creating layers and layered interfaces between periodic structures.
 - New panel for extracting dimer structures from a periodic system.
 - New panel to easily setup Desmond Molecular Dynamics simulations.
 - New hyperbola fitting method in Thermophysical Analysis panel for Tg calculation and convergence check


평가판 (Evaluation) 신청: https://www.schrodinger.com/salescenter/

Announcing Schrödinger Software Release 2015-2

게시자: Quantum Bio Solutions LLC, 2015. 5. 19. 오전 1:25   [ 2015. 5. 31. 오후 8:47에 업데이트됨 ]

-. Schrödinger Software Release 2015-2 버전이 업데이트 되었습니다.

-. Schrödinger Software Release 2015-2 버전 다운로드 받기 (https://www.schrodinger.com/downloadcenter/25)

-. Schrödinger Software Release 2015-2 버전에서 향상된 내용은 아래 설명을 참고하시기 바랍니다.

Maestro: Graphical Interface

    Large speed improvements displaying objects in the Workspace [ 2015-2 ]

Maestro: Molecular Dynamics

    Added support for running simulations on Nvidia Tesla K-80 GPUs [ 2015-2 ]

Maestro: Ligand Docking

    Dock ligands directly from a Phase database including subset support [ 2015-2 ]

Maestro: Covalent Ligand Docking

    User adjustable XYZ grid center [ 2015-2 ]
    Optionally calculate MM-GBSA energy on the pre-reacted complex (command line only) [ 2015-2 ]

Maestro: Quantum Mechanics

    Specify the number of simultaneous calculations in batch jobs [ 2015-2 ]
    New interface and support for running commercial MOPAC2012 [ 2015-2 ]

Maestro: ADME Prediction

    Accuracy improvements to Physics-based Membrane Permeability predictions [ 2015-2 ]
    Physics-based Membrane Permeability now automatically employs the optimal sampling protocol for macrocyclic and non-macrocyclic ligands [ 2015-2 ]

Workflows & Pipelining

    Includes the latest version of KNIME (v2.11.3) [ 2015-2 ]
    New Multiple Sequence Viewer node [ 2015-2 ]

BioLuminate
       
    Non-native amino acid support in residue scanning and affinity maturation [ 2015-2 ]
    Significantly faster SlogP calculation [ 2015-2 ]
    Improved consistency of reference and mutation states in Affinity Maturation [ 2015-2 ]

Materials Science Suite:
       
    Improvements in bonding treatments in crystal structure building [ 2015-2 ]
    New panel for Amorphous NMR calculations [ 2015-2 ]
    Display Atoms toolbar added to the list of available toolbars [ 2015-2 ]
    New Thermophysical Properties Setup and Analysis panels for computing density, coefficient of thermal expansion and Tg [ 2015-2 ]
    Slab builder command line script to create slabs and surfaces from crystal structures [ 2015-2 ]
        $SCHRODINGER/run surface.py

 Materials Science Suite: Disordered System Builder

    Disordered System Builder has two new options [Monte Carlo simulated annealing and Minimization] to relax the system in addition to the existing steric pack method [ 2015-2 ]
    Disordered System Builder can now build to a target density [ 2015-2 ]
    Disordered System Builder can create systems around, inside or at an interface with a substrate [ 2015-2 ]

Materials Science Suite: Genetic Algorithm

    Genetic Optimization can now block H2 from entering the population [ 2015-2 ]
    Genetic Optimization now uses a freezer of structures to pull from to replace bad structures in the population [ 2015-2 ]
    Genetic Optimization can now perform a conformational search on each new structure [ 2015-2 ]

Materials Science Suite: Nanoparticle Builder

    Nanoparticle Builder no longer fragments molecules at the particle boundary [ 2015-2 ]
    Nanoparticle Builder shape is now previewed in the workspace and the user can give it a custom orientation [ 2015-2 ]

♣ Organic semiconductor electron coupling in the condensed phase using the Schrödinger Materials Science Suite

게시자: Quantum Bio Solutions LLC, 2015. 5. 7. 오전 3:20

♣ Organic semiconductor electron coupling in the condensed phase using the Schrödinger Materials Science Suite
Dr. Alexander Goldberg (Senior Scientist)
 
 
 
Organic semiconductors (OSC) are under widespread investigation to displace or complement inorganic optoelectronic devices for photovoltaic and display applications.
In the development of OSC materials, of equal importance to the intrinsic molecular electronic properties, is the injection and transport of electrons within the active layers comprising the device. Recently, we have implemented a direct electron coupling algorithm in our Jaguar DFT program and an automated coupling analysis workflow in the Schrödinger Materials Science Suite. These tools allow the efficient analysis of donor-acceptor pairs from an atomistic morphology calculated using classical molecular dynamics, providing additional insight into the factors impacting OSC performance. In this presentation, the dependence of the electron coupling on basis set, density functionals, and reference input wavefunctions is discussed. Also, comparisons of the electron coupling for ordered and amorphous systems are presented.

자세한 내용의 세미나 동영상은 다음 링크에서 보실 수 있습니다.

Announcing Schrödinger Software Release 2015-1

게시자: Quantum Bio Solutions LLC, 2015. 3. 30. 오전 9:45

We are pleased to announce Schrödinger software release 2015-1.
This quarterly release includes usability improvements and performance enhancements across all of our software.

Schrödinger Software 2014-4 버전 출시

게시자: Quantum Bio Solutions LLC, 2014. 11. 12. 오후 11:17   [ 2014. 11. 16. 오후 7:52에 업데이트됨 ]

 
Schrödinger Software 2014-4 버전이 출시되었습니다.
신규 버전은 다음 링크에서 다운로드 받으실 수 있습니다. (https://www.schrodinger.com/downloadcenter/25)

New Features & Enhancements의 간략한 내용은 다음과 같습니다.
 
  Maestro Graphical Interface
  • Control alignment in flexible ligand analysis by specifying core atoms via Bemis-Murcko scaffold, MCS, or SMARTS [ 2014-4 ]
  • Hierarchical display of jobs in the Job Monitor panel [ 2014-4 ]
  • Ligand detection options moved to Preferences panel [ 2014-4 ]
  • Create entry from Workspace now places new entry directly after the source entry [ 2014-4 ]
  Ligand Preparation and Conformation Generation
  • Improved speed of ring template generation [ 2014-4 ]
  • Identify the most probable neutral state when generating states by using -best_neutral and -best_neutral_zwit arguments (command line only) [ 2014-4 ]
  Empirical and QM-based pKa Prediction
  • Improved accuracy of Epik pKa predictions with better treatment of resonance effects [ 2014-4 ]
  Quantum Mechanics
  • Geometry optimization relaxes local saddle points to help arrive at a true minimum [ 2014-4 ]
  • Jaguar incorporates links to input, output, log, and restart files for a simplified tracking of settings and files[2014-4]
  Protein Refinement
  • Upgraded homology modeling in both the Workflow Wizard and the Multiple Sequence Viewer to BLAST+ [ 2014-4 ]
  Ligand Docking
  • Dock ligands from a Phase database, including support for docking subsets of ligands (command line only)[2014-4]
  ADME Prediction
  • Enhanced sampling of macrocycle conformations in membrane permeability predictions [ 2014-4 ]
  Covalent Ligand Docking
  • Allow attachment of docked ligand to a non-standard receptor residue, such as non-native amino acids, DNA, cofactors, or another ligand [ 2014-4 ]
  Biologics Suite
  • Improved similarity of Residue Scanning and Affinity Maturation user interfaces for enhanced usability and a more intuitive workflow [ 2014-4 ]
  • Several improvements to Residue Scanning user interface [ 2014-4 ]
    • - Request residue mutations for residues in different chains within one simulation
    - In Homology Suggestions, clarify ability to use sequences without 3D structure
    - In Homology Suggestions, support antibody annotation in the sequence viewer
  • Several improvements to the Antibody Modeling user interface [ 2014-4 ]
    • - Select numbering scheme for calculations from: Chothia, Enhanced Chothia, Kabat, IMGT, and AHo
    - Allow user to predict either Fv, Fab, or full antibody including Fc
    - Show loop source when non-default is selected
    - Show more information on loop choices throughout interface
    - Optionally override default residues defining the beginning or end of each loop
  Materials Science Suite
  • Improved Multiple Complex Builder to handle heteroleptic complexes [ 2014-4 ]
  • New nanoparticle command line utility for creating spherical and polyhedron particles from crystals [ 2014-4 ]
  • New nanoparticle GUI for the command line utility functionality [ 2014-4 ]
  • New capabilities in Bond and Ligand Dissociation panel for specifying bonds to include or ignore [ 2014-4 ]
  • Polymer Builder can now create amorphous cells ready for Desmond runs [ 2014-4 ]
  • Added Crystal Planes by Miller Index to Periodicity Toolbar   [ 2014-4 ]
보다 자세한 내용은 다음 링크에서 확인하시기 바랍니다. (http://www.schrodinger.com/newfeatures/)
 

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