From 94240eddb9069ed2452e718094364f7524b52f38 Mon Sep 17 00:00:00 2001 From: Debasish Mukherjee <35124770+MDebasish@users.noreply.github.com> Date: Wed, 7 Feb 2018 06:49:27 +0000 Subject: [PATCH] Create README.md README file added --- README.md | 138 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 138 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..0916316 --- /dev/null +++ b/README.md @@ -0,0 +1,138 @@ +BPFind v. 1.8 +(http://www.saha.ac.in/biop/dhananjay.bhattacharyya/bpfind.tar.gz) + +Please cite the reference while using BPFind tool: + +Non-canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal +Structure Database Analysis(2006), +Das, J.; Mukherjee, S.; Mitra, A.; Bhattacharyya, D., J. Biomol. Struct. Dynam., +24,149. + + +(For any query, please mail to: dhananjay.bhattacharyya@saha.ac.in) + + +BPFind is a software tool for detecting stable and feasible basepairs present in +nucleic acid molecules. It finds potential H-bonds within the molecule and +checks for the basepair geometry to output the best possible pairing pattern +between a pair of bases. BPFind considers both the standard N/O-H...N/O and +non-polar C-H...O/N types of hydrogen bonding. However, one can also detect +those basepairs stabilized only by regular polar hydrogen bonds. + + +1. Input File Type: +------------------- + +Files containing coordinates of the atoms in PDB format (XXXX.pdb). + +2. Output File Description: +--------------------------- + +XXXX.cor - Contains coordinates of the nucleic acids only considered for + searching H-bonds. Base moieties, not having all the + purine/pyrimidine ring atoms and C1' atoms, are not considered for + basepairing. Therefore, they are not included in XXXX.cor files. +XXXX.out - Contains detailed descriptions of the basepairing patterns present + within the RNA molecule.Format is as below: +XXXX.nup - Contains basepairing information required to run the associated + basepair parameter calculation program NUPARM. The NUPARM software + can also be downloaded from the same site. +XXXX.dat - Contains base pairing information of each nucleotide residue in + symple format, such as H for Watson-Crick basepairs, N for non- + canonical basepairs, T for base triples and L for nonpaired bases +XXXX.hlx - Contains base pairing information of only the double helices, + ignoring the unpaired as well as isolated pairs. + +The XXXX.out file gives the basepairing informations in the following way: +================================================================================ +Column starting from '>' mark represent the following: +>Serial number of nucleotides +----->Residue number as in PDB +---------->Residue name +--------------->Chain ID +---------------->Serial number of the paired base +--------------------->Residue number of the paired base as in PDB +-------------------------->Residue name of the paired base +------------------------------->Chain ID of the paired base +--------------------------------->Base pair type +-------------------------------------->Base pair indicator +--------------------------------------->E-value indicating base pair deformation +------------------------------------------->Equivalent info for other pairs +================================================================================ + +XXXX.fasta - Contains sequence of the nucleotide chains in a PDB file with + residues having coordinates of all ring atoms and C1' atom. + +XXXX.hlx - Contains the pseudo-continuous stack regions in the nucleic acid + molecule as given by their BPFind numbering. + + + +3. Abbreviations Used in Output Files: +-------------------------------------- + +W - Watson-Crick edge +H - Hoogsteen edge +S - Sugar edge +w - Watson-Crick edge with one or more C-H...O/N type of hydrogen bond +h - Hoogsteen edge with one or more C-H...O/N type of hydrogen bond +s - Sugar edge with one or more C-H...O/N type of hydrogen bond ++ - Protonated Watson-Crick edge +z - Protonated Sugar edge +C - Cis +T - Trans + + +4. Runtime Options: +------------------- + +USAGE: BPFIND -[options] filename + +The following options can be used: +-HD [value] to set default hydrogen bond distance cutoff (default = 3.8) +-VA [value] to set default pseudo angle cutoff (default = 120.0) +-EN [value] to set default E-value cutoff (default = 1.8) +-HT to include HETATM entries in PDB +-CH to avoid identification of base pairs stabilized by C-H...O/N H-bonds +-SG to avoid identification of base pairs involving sugar O2' atoms +-AB to avoid base pairing between residue no. i and i+1 +-OL to avoid printing base pairing information w.r.t.the second strand. + This is suitable for simple oligonucleotides +-ML [character] to detect base pairing within a particular selected chain of DNA/RNA +-NMR to calculate base pairing information for the first model in NMR derived +ensemble of structures + +5. Basepairing Criteria: +------------------------ + +BPFind maintains a few criteria for detecting basepairs: + +(i) Bases not having coordinates of all the ring atoms (purine/pyrimidine) and + C1' atoms are not considered for detecting hydrogen bonds. +(ii) At least two hydrogen bonds must exist between two bases, at least one of + which must be between the base moieties. Basepairs involving both 2'-OH + mediated hydrogen bonds are not detected by BPFind. It considers basepairs + for which both the H-bonds are of C-H...O/N type, as long as one H-bond is + found between the base rings. +(iii) BPFind considers a range of modified bases which are usually under the + 'HETATM' lines in a PDB file. They are listed in the four files: + AdeVariants.name + Guavariants.name + CytVariants.name + UraVariants.name + We keep these files in /usr/local/bin directory and the program also + expects them there. In case you want to keep them somewhere else, + please modify the code (line nos. 57, 65, 73 and 81) to indicate the + location of these files. + Any new modified residue name can be included in one of these files + accordingly in order to be recognized by BPFind. +(iv) BPFind uses a cutoff distance of 3.8 angstrom between the acceptor and + donor atoms, a cutoff angle of 120.0 degree for checking planarity of + precursor atoms (designed carefully to accommodate more labile basepairs) + and a cutoff E-value of 1.8 to signify the overall distortion and maintain + a good basepairing geometry. +(v) BPFind uses a more stringent option for protonated basepair options in + order to avoid false positives. It considers cutoff angle of 150.0 degree + for protonated basepairs. +(vi) BPFind allows more flexibility if 2'-OH of the ribose sugar moiety is + involved in hydrogen bonding - a cutoff angle of 100.0 degree.