Search Results for "option"

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other...

- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -...

Updated 2022-06-11 added option to allow use of atoms other than C-alpha Updated 2021-11-29 to enable compilation on stricter compilers. Ab Initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. Calibur is an efficient tool for finding the decoy with the most number of neighbors within a threshold distance.

A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat.

...For comparison purposes, non-SSMD-based methods such as percent activity, z-score, and t-test are also provided as scoring options. Version 2.1 released: several bugs fixed. Version 3.0 released for Windows and Mac: experiment-wise analysis option, map to all samples option (no hit cut-off needed), percent activity for replicates option and .ai output format are added

FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron). If you have Emboss, you can genarate a graphic with option -graph 1. Dependencies: - Perl - Bioperl - UNIX system - tfasty - Emboss (if you want a graphic)

slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. The slclust utility is written in ANSI C++.

NoBlast provides a new extended user friendly csv output format and offers an option to correct the statistics when split databases are used for NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx).