Molmil: a molecular viewer for the PDB and beyond

被引：59

作者：

Bekker, Gert-Jan ^{[1
,2
]}

Nakamura, Haruki ^{[1
]}

Kinjo, Akira R. ^{[1
]}

机构：

[1] Osaka Univ, Inst Prot Res, Lab Prot Informat, 3-2 Yamadaoka, Suita, Osaka 5650871, Japan

[2] Osaka Univ, Grad Sch Frontier Biosci, Suita, Osaka 5650871, Japan

来源：

JOURNAL OF CHEMINFORMATICS | 2016年 / 8卷

关键词：

WebGL; Protein structure visualization; Molecular dynamics; PROTEIN DATA-BANK; DYNAMICS; REPRESENTATION; VISUALIZATION; FORMAT;

D O I：

10.1186/s13321-016-0155-1

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

引用

页数：5

共 19 条

[1] Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers [J].

Abraham, Mark James ;

Murtola, Teemu ;

Schulz, Roland ;

Páll, Szilárd ;

Smith, Jeremy C. ;

Hess, Berk ;

Lindah, Erik .

SoftwareX, 2015, 1-2 :19-25

[2]

Fitzgerald PMD, 2006, INT TABLES CRYSTALLO, P295

[3] THE STAR FILE - A NEW FORMAT FOR ELECTRONIC DATA TRANSFER AND ARCHIVING [J].

HALL, SR .

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1991, 31 (02) :326-333

[4] JS']JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia [J].

Hanson, Robert M. ;

Prilusky, Jaime ;

Renjian, Zhou ;

Nakane, Takanori ;

Sussman, Joel L. .

ISRAEL JOURNAL OF CHEMISTRY, 2013, 53 (3-4) :207-216

[5] Jmol - a paradigm shift in crystallographic visualization [J].

Hanson, Robert M. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2010, 43 :1250-1260

[6] VMD: Visual molecular dynamics [J].

Humphrey, W ;

Dalke, A ;

Schulten, K .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1996, 14 (01) :33-38

[7] Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format [J].

Kinjo, Akira R. ;

Suzuki, Hirofumi ;

Yamashita, Reiko ;

Ikegawa, Yasuyo ;

Kudou, Takahiro ;

Igarashi, Reiko ;

Kengaku, Yumiko ;

Cho, Hasumi ;

Standley, Daron M. ;

Nakagawa, Atsushi ;

Nakamura, Haruki .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D453-D460

[8] eF-site and PDBjViewer: database and viewer for protein functional sites [J].

Kinoshita, K ;

Nakamura, H .

BIOINFORMATICS, 2004, 20 (08) :1329-1330

[9] YASARA View-molecular graphics for all devices-from smartphones to workstations [J].

Krieger, Elmar ;

Vriend, Gert .

BIOINFORMATICS, 2014, 30 (20) :2981-2982

[10] Control over overall shape and size in de novo designed proteins [J].

Lin, Yu-Ru ;

Koga, Nobuyasu ;

Tatsumi-Koga, Rie ;

Liu, Gaohua ;

Clouser, Amanda F. ;

Montelione, Gaetano T. ;

Baker, David .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (40) :E5478-E5485

← 1 2 →