README.md

# ASDP ReadMe

ASDP is an automated NMR NOE assignment engine. It uses a distinct bottom-up topology-constrained approach for iterative NOE interpretation and generates 3D structures of the protein that is as close to the true structure as possible.

### Initial Fold Analysis

ASDP first builds an initial chain fold based on intraresidue and sequential NOESY data, characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unambiguous long-range NOE interactions, based on chemical shift matching and NOESY spectral symmetry considerations. "Ambiguous constraints" are not used in the initial structure calculations.

### Iterative Fold Analysis

ASDP generates distance constraint lists and utilizes the programs CYANA, or Xplor for 3D structure generation, and CNSw for refinement on a Linux-based computer cluster. DP scores (Huang et al, JACS 127:1665-74, 2005) are calculated for all intermediate models. Only the top models with highest DP scores and lowest target function (CYANA) or conformational energy (XPLOR) values are selected for iterative NOE analysis. After two cycles of model generation with CYANA or XPLOR and model selection with DP filter, NOESY cross peaks are iteratively assigned using the intermediate 3D structures and contact maps, together with knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. Using a DP filter for model selection improves the accuracy of the selected intermediate structures for iterative NOE analysis and therefore improves the accuracy of NOESY crosspeak assignments and final models.

### Bottom Up Strategy

The ASDP protocol, in principle, resembles the method that an expert would utilize in manually solving a protein structure by NMR. ASDP "bottom up" strategy is quite different from the "top down" strategies used by programs CANDID and ARIA, which rely on "ambiguous constraints". For NOESY spectra with poor signal-to-noise ratios, such automatically assigned "ambiguous constraints" sets may not include any true NOESY assignments, and result in small distortions of the protein structure which may be avoided by the "bottom up" approach of ASDP. CANDID/CYANA also uses a "network anchoring" approach similar to, but less comprehensive than, the topology-constrained approach used by ASDP. For these reasons, some users may prefer to use both ASDP and CANDID/CYANA or ARIA in parallel to assess potential errors in automated NOESY cross peak assignments.


#### For citing ASDP you may consider:

Huang, Y. J.; Tejero, R.; Powers, R.; Montelione, G.T. A topology-constrained distance network algorithm for protein structure determination from NOESY data. PROTEINS: Struct. Funct. Bioinformatics 15, 587-603 (2006)

Huang, Y.J., Mao, B., Xu, F., and Montelione, G.T. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score. J. Biomol. NMR, 62: 439-451, 2015.

### RPF/DP 

RPF uses a novel, rapid, and simple approach for calculating global NMR structure quality scores. This program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores assessing how well the query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data. RPF scores quickly assess the goodness-of-fit of the query structure(s) to these experimental data, and can be used as a guide for further structure refinements. RPF also calculates discrimination power(DP) scores, which estimate the difference in F-MEASURE scores between the query structure and "random coil" structures, as an indictor of the correctness of the overall fold.

#### For citing RPF you may consider:

Huang, Y. J.; Powers, R. & Montelione, G. T. Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127, 1665-74 (2005)


## 1. Compile C/C++source code:

Two programs noesyassign and pdbstat are written in C/C++.

noesyassign:

	go to noeysassign/src/Release/ directory and type 'make noesyassign'

pdbstat:

	go to PDBSTAT/src directory and type `make` to follow the instruction.


## 2. Setup ASDP runs with clusters, cyana and xplor

a. Edit the file 'env.sh' for your computer system.

b. run "./config.pl"

c. Cluster

You may also need to edit the queue configuration file under 'queue' directory. If you are using PBS, edit file 'queue/PBS.pm'. If you are using SLURM, edit file 'queue/SLURM.pm'. If you are using something else, you need to work on file 'Custom.pm', change the queue_header to fit your system.

d. EC-NMR

cyana/openmpi compiled version is required if running on a cluster

e. perl/TK

In order to use the graphical user interface version of ASDP, you must have perl/TK installed.  TK can be downloaded and installed from http://search.cpan.org.  The command line version does not require TK.

## 3. How to run ASDP

a quick start: (https://github.rpi.edu/RPIBioinformatics/ASDP_public/blob/main/Tutorial.md)

For most of the programs, you may type the command for help.

asdp -> run in command-line

asdp-gui -> run with GUI interface

CreateProc -> Setup structure calculations with Cyana or Xplor on a cluster


Other tools:

bmrb2lacs.pl -> convert bmrb file to lacs input format (bija.nmrfam.wisc.edu/MANI-LACS/).

bmrb2talos.pl -> convert bmrb file to talos input format.

talos2aco.pl -> convert talos output to dihedral angle file in cyana format



## 4. Prepare Input

See examples directory

A. resonance assignment files in bmrb 2.1 or 3.1 format

B. peak lists

C. control-file (use asdp-gui to prepare or see examples)


## 5. Examples:

Visit https://github.rpi.edu/RPIBioinformatics/ASDP_public/blob/main/Tutorial.md#4-data-in-the-examples-directory-contributed-by-the-casd-nmr for more info.

CtR69A:

	asdp run with cyana: asdp -c control_fileCyana -o runCyana
	asdp run with xplor: asdp -c control_fileXplor -o runXplor


oxidized_ET109 - it has a disulfide bond, a HIST with RDC data

	HIST is defined in the chemical shift file (final.bmrb) and special.lib
	Disulfide bond and RDC are defined in the control_fileNoCns file.
	Step 1: asdp run: asdp -c control_fileCyana -o runCyana
	Step 2: run CNSw Refinement

taf3 - it has two ZNs. one binds to 21C,24C,44H, 47C, and another binds to 36C,39C,62C,65C
	Zn binding residue modification - defined in the chemical shift file (final.bmrb) and special.lib

	Zn geometry constraints are zn_dist2.lol and zn_dist2.upl
	asdp run with no Cns: asdp -c control_filesCyana -o runCyana