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{| class="wikitable sortable"
|-
! Name
! View 3D
! Model build
! Min
! MD
! MC
! REM
! Crt
! Int
! Exp
! Imp
! Lig
! GPU
! Comments
! [[Software license|License]]
! Website
|-
| [[Abalone (molecular mechanics)|Abalone]]
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || [[DNA]], [[protein]]s, [[Ligand (biochemistry)|ligands]] || {{free}} || [http://www.biomolecular-modeling.com/Abalone/ Agile Molecule]
|-
| [[AMBER]]<ref>{{cite journal |
doi=10.1021/ja00124a002 |author1=Cornell W.D. |author2=Cieplak P. |author3=Bayly C.I. |author4=Gould I.R. |author5=Merz K.M., Jr. |author6=Ferguson D.M. |author7=Spellmeyer D.C. |author8=Fox T. |author9=Caldwell J.W. |author10=Kollman P.A. |
title=A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules |
journal= J. Am. Chem. Soc. |volume=117 |issue=19 |pages=5179–5197 |year=1995|citeseerx=10.1.1.323.4450 }}</ref>
| {{no}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{yes}} || {{yes}}<ref>http://ambermd.org/GPUSupport.php</ref> || [[AMBER]] [[Force field (chemistry)|force field]] || {{proprietary}} || [http://ambermd.org ambermd.org]
|-
| [[Ascalaph Designer]]
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || [[AMBER]] || {{free}}, [[GNU General Public License|GPL]] || [http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html biomolecular-modeling.com]
|-
| [[CHARMM]]
| {{no}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || CHARMM [[Force field (chemistry)|force field]] || {{proprietary}} || [http://www.charmm.org/ charmm.org]
|-
| Forecaster (Fitted)<ref>{{cite journal |last1=Wei |first1=Wanlei |last2=Luo |first2=Jiaying |last3=Waldispühl |first3=Jérôme |last4=Moitessier |first4=Nicolas |title=Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes |journal=Journal of Chemical Information and Modeling |date=24 June 2019 |volume=59 |issue=6 |pages=2941–2951 |doi=10.1021/acs.jcim.9b00163 |pmid=30998377 |issn=1549-960X}}</ref>
| {{yes}} || {{no}} || {{yes}} || {{no}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || Small molecule docking to nucleic acids with water placement || Free for academia, [[Proprietary software|Proprietary]] || [https://www.molecularforecaster.com/products#drug-discovery-anchor Molecular Forecaster]
|-
| [[HyperChem]]
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || some force fields || {{proprietary}} || [http://www.hyper.com/ Hypercube, Inc.]
|-
| ICM<ref>{{cite journal |
doi=10.1002/jcc.540150503 |author1=Abagyan R.A., Totrov M.M. |author2=Kuznetsov D.A. |lastauthoramp=yes|
title=Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation |
journal=J. Comput. Chem. |volume=15 |issue=5 |pages=488–506 |year=1994}}</ref>
| {{yes}} || {{yes}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{no}} || [[Global optimization]] || {{proprietary}} || [http://www.molsoft.com Molsoft]
|-
| JUMNA<ref>{{cite journal |
doi=10.1016/0010-4655(95)00046-I |
author=Lavery, R., Zakrzewska, K. and Sklenar, H. |
title=JUMNA: junction minimisation of nucleic acids |
journal= Comput. Phys. Commun. |volume=91 |
issue=1–3 |pages=135–158 |year=1995 |bibcode= 1995CoPhC..91..135L}}</ref>
| {{no}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{no}} || <!--comments--> || {{proprietary}} ||
|-
| [[MDynaMix]]<ref>{{cite journal |
doi= 10.1016/S0010-4655(99)00529-9 |
title= MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures |
author= A.P.Lyubartsev, A.Laaksonen |
journal= Computer Physics Communications |volume= 128 |
issue= 3 |year=2000 |pages= 565–589 |bibcode= 2000CoPhC.128..565L}}</ref>
| {{yes}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || Common MD || {{free}}, [[GNU General Public License|GPL]] || [http://www.fos.su.se/~sasha/mdynamix/ Stockholm University]
|-
| [[Molecular Operating Environment]] (MOE)
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || <!--comments--> || {{proprietary}} || [http://www.chemcomp.com/ Chemical Computing Group]
|-
| Nucleic Acid Builder (NAB)<ref>{{cite journal |author1=Macke T. |author2=Case D.A. |lastauthoramp=yes|
title= Modeling unusual nucleic acid structures |
journal= Molecular Modeling of Nucleic Acids |
pages=379–393 |year=1998}}</ref>
| {{no}} || {{yes}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || {{no}} || Generates models for unusual DNA, RNA || {{free}}, [[GNU General Public License|GPL]] || [http://casegroup.rutgers.edu New Jersey University]
|-
| NAnoscale Molecular Dynamics ([[NAMD]])
| {{yes}} || {{no}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{yes}} || Fast, parallel MD, CUDA || {{free}} || [http://www.ks.uiuc.edu/Research/namd/ University of Illinois]
|-
| oxDNA<ref>{{cite journal |
doi= 10.1063/1.4754132 |pmid=23039613 |author1=Petr Šulc |author2=Flavio Romano |author3=Thomas E. Ouldridge |author4=Lorenzo Rovigatti |author5=Jonathan P. K. Doye |author6=Ard A. Louis |
title= Sequence-dependent thermodynamics of a coarse-grained DNA model |
journal= J. Chem. Phys. |volume=137 |issue=13 |
pages=135101 |year=2012|arxiv=1207.3391 |bibcode=2012JChPh.137m5101S }}</ref>
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || Coarse-grained models of DNA, RNA || {{free}}, [[GNU General Public License|GPL]] || [http://dna.physics.ox.ac.uk dna.physics.ox.ac.uk][https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna LAMMPS USER-CGDNA]
|-
|QRNAS <ref>{{Cite journal|last=Stasiewicz|first=Juliusz|last2=Mukherjee|first2=Sunandan|last3=Nithin|first3=Chandran|last4=Bujnicki|first4=Janusz M.|date=2019-03-21|title=QRNAS: software tool for refinement of nucleic acid structures|journal=BMC Structural Biology|volume=19|issue=1|pages=5|doi=10.1186/s12900-019-0103-1|pmid=30898165|issn=1472-6807|pmc=6429776}}</ref>
| {{No}} || {{No}} || {{Yes}} || {{No}} || {{No}} || {{No}} || {{Yes}} || {{No}} || {{No}} || {{Yes}} || {{No}} || {{No}} || High resolution refinement of models of [[RNA]], [[DNA]] and hybrids using [[AMBER]] [[Force field (chemistry)|force field]] . ||{{free}}, [[GNU General Public License|GPL]] || [http://genesilico.pl/software/stand-alone/qrnas Genesilico] [https://github.com/sunandanmukherjee/QRNAS.git Github]
|-
|SimRNA<ref>{{Cite journal|last=Boniecki|first=Michal J.|last2=Lach|first2=Grzegorz|last3=Dawson|first3=Wayne K.|last4=Tomala|first4=Konrad|last5=Lukasz|first5=Pawel|last6=Soltysinski|first6=Tomasz|last7=Rother|first7=Kristian M.|last8=Bujnicki|first8=Janusz M.|date=2015-12-19|title=SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction|journal=Nucleic Acids Research|volume=44|issue=7|pages=e63|doi=10.1093/nar/gkv1479|pmid=26687716|issn=0305-1048|pmc=4838351}}</ref>
| {{yes}} || {{yes}} || {{No}} || {{No}} || {{Yes}} || {{Yes}} || {{Yes}} || {{Yes}} || {{No}} || {{Yes}} || {{No}} || {{No}} || Coarse grained modeling of RNA || Free for Academic, [[Proprietary software|Proprietary]]|| [http://genesilico.pl/software/stand-alone/simrna Genesilico]
|-
|SimRNAweb<ref>{{Cite journal|last=Magnus|first=Marcin|last2=Boniecki|first2=Michał J.|last3=Dawson|first3=Wayne|last4=Bujnicki|first4=Janusz M.|date=2016-04-19|title=SimRNAweb: a web server for RNA 3D structure modeling with optional restraints|journal=Nucleic Acids Research|volume=44|issue=W1|pages=W315–W319|doi=10.1093/nar/gkw279|pmid=27095203|pmc=4987879|issn=0305-1048}}</ref>
| {{yes}} || {{yes}} || {{No}} || {{No}} || {{Yes}} || {{Yes}} || {{Yes}} || {{Yes}} || {{No}} || {{Yes}} || {{No}} || {{No}} || Coarse grained modeling of RNA |||Free || [https://genesilico.pl/SimRNAweb/ Genesilico]
|-
| [[YASARA]]
| {{yes}} || {{yes}} || {{yes}} || {{yes}} || {{no}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || {{yes}} || {{no}} || Interactive simulations || {{proprietary}} || [http://www.yasara.org www.YASARA.org]
|-
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== Ayrıca bakınız ==
== Ayrıca bakınız ==

Sayfanın 17.47, 14 Nisan 2020 tarihindeki hâli

Bu liste, nükleik asit simülasyonları için kullanılan bilgisayar programlarının bir listesidir.

Name View 3D Model build Min MD MC REM Crt Int Exp Imp Lig GPU Comments License Website
Abalone Evet Evet Evet Evet Evet Evet Evet Hayır Evet Evet Evet Evet DNA, proteins, ligands Şablon:Free Agile Molecule
AMBER[1] Hayır Evet Evet Evet Hayır Evet Evet Hayır Evet Evet Evet Evet[2] AMBER force field Tescilli ambermd.org
Ascalaph Designer Evet Evet Evet Evet Hayır Hayır Evet Hayır Evet Evet Evet Hayır AMBER Şablon:Free, GPL biomolecular-modeling.com
CHARMM Hayır Evet Evet Evet Evet Hayır Evet Hayır Evet Evet Evet Hayır CHARMM force field Tescilli charmm.org
Forecaster (Fitted)[3] Evet Hayır Evet Hayır Hayır Hayır Evet Hayır Evet Hayır Evet Hayır Small molecule docking to nucleic acids with water placement Free for academia, Proprietary Molecular Forecaster
HyperChem Evet Evet Evet Evet Evet Hayır Evet Hayır Evet Evet Evet Hayır some force fields Tescilli Hypercube, Inc.
ICM[4] Evet Evet Evet Hayır Evet Hayır Hayır Evet Hayır Evet Hayır Hayır Global optimization Tescilli Molsoft
JUMNA[5] Hayır Evet Evet Hayır Hayır Hayır Hayır Evet Hayır Evet Hayır Hayır Tescilli
MDynaMix[6] Evet Evet Hayır Evet Hayır Hayır Evet Hayır Evet Hayır Evet Hayır Common MD Şablon:Free, GPL Stockholm University
Molecular Operating Environment (MOE) Evet Evet Evet Evet Hayır Hayır Evet Hayır Evet Hayır Evet Hayır Tescilli Chemical Computing Group
Nucleic Acid Builder (NAB)[7] Hayır Evet Hayır Hayır Hayır Hayır Hayır Hayır Hayır Hayır Hayır Hayır Generates models for unusual DNA, RNA Şablon:Free, GPL New Jersey University
NAnoscale Molecular Dynamics (NAMD) Evet Hayır Evet Evet Hayır Hayır Evet Hayır Evet Hayır Evet Evet Fast, parallel MD, CUDA Şablon:Free University of Illinois
oxDNA[8] Evet Evet Evet Evet Evet Evet Evet Hayır Hayır Evet Hayır Evet Coarse-grained models of DNA, RNA Şablon:Free, GPL dna.physics.ox.ac.ukLAMMPS USER-CGDNA
QRNAS [9] Hayır Hayır Evet Hayır Hayır Hayır Evet Hayır Hayır Evet Hayır Hayır High resolution refinement of models of RNA, DNA and hybrids using AMBER force field . Şablon:Free, GPL Genesilico Github
SimRNA[10] Evet Evet Hayır Hayır Evet Evet Evet Evet Hayır Evet Hayır Hayır Coarse grained modeling of RNA Free for Academic, Proprietary Genesilico
SimRNAweb[11] Evet Evet Hayır Hayır Evet Evet Evet Evet Hayır Evet Hayır Hayır Coarse grained modeling of RNA Free Genesilico
YASARA Evet Evet Evet Evet Hayır Hayır Evet Hayır Evet Hayır Evet Hayır Interactive simulations Tescilli www.YASARA.org

Ayrıca bakınız

Kaynakça

  1. ^ Cornell W.D.; Cieplak P.; Bayly C.I.; Gould I.R.; Merz K.M., Jr.; Ferguson D.M.; Spellmeyer D.C.; Fox T.; Caldwell J.W.; Kollman P.A. (1995). "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules". J. Am. Chem. Soc. 117 (19): 5179–5197. CiteSeerX 10.1.1.323.4450 $2. doi:10.1021/ja00124a002. 
  2. ^ http://ambermd.org/GPUSupport.php
  3. ^ Wei, Wanlei; Luo, Jiaying; Waldispühl, Jérôme; Moitessier, Nicolas (24 June 2019). "Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes". Journal of Chemical Information and Modeling. 59 (6): 2941–2951. doi:10.1021/acs.jcim.9b00163. ISSN 1549-960X. PMID 30998377. 
  4. ^ Abagyan R.A., Totrov M.M.; Kuznetsov D.A. (1994). "Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation". J. Comput. Chem. 15 (5): 488–506. doi:10.1002/jcc.540150503.  Kaynak kaldırılmış |lastauthoramp= parametresini kullanıyor (yardım)
  5. ^ Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comput. Phys. Commun. 91 (1–3): 135–158. Bibcode:1995CoPhC..91..135L. doi:10.1016/0010-4655(95)00046-I. 
  6. ^ A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128 (3): 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9. 
  7. ^ Macke T.; Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.  Kaynak kaldırılmış |lastauthoramp= parametresini kullanıyor (yardım)
  8. ^ Petr Šulc; Flavio Romano; Thomas E. Ouldridge; Lorenzo Rovigatti; Jonathan P. K. Doye; Ard A. Louis (2012). "Sequence-dependent thermodynamics of a coarse-grained DNA model". J. Chem. Phys. 137 (13): 135101. arXiv:1207.3391 $2. Bibcode:2012JChPh.137m5101S. doi:10.1063/1.4754132. PMID 23039613. 
  9. ^ Stasiewicz, Juliusz; Mukherjee, Sunandan; Nithin, Chandran; Bujnicki, Janusz M. (2019-03-21). "QRNAS: software tool for refinement of nucleic acid structures". BMC Structural Biology. 19 (1): 5. doi:10.1186/s12900-019-0103-1. ISSN 1472-6807. PMC 6429776 $2. PMID 30898165. 
  10. ^ Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M. (2015-12-19). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351 $2. PMID 26687716. 
  11. ^ Magnus, Marcin; Boniecki, Michał J.; Dawson, Wayne; Bujnicki, Janusz M. (2016-04-19). "SimRNAweb: a web server for RNA 3D structure modeling with optional restraints". Nucleic Acids Research. 44 (W1): W315–W319. doi:10.1093/nar/gkw279. ISSN 0305-1048. PMC 4987879 $2. PMID 27095203. 
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