\section{TECHNICAL SUPPORT CONTACT INFORMATION}
\label{sect:support}
- Dawid Jagie{\l}a\\
+ Cezary Czaplewski\\
Faculty of Chemistry, University of Gdansk\\
ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
- fax: +48 58 523 5012\\
- e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\
+ fax: +48 58 523 5128\\
+ e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}\\
+
+ Adam K. Sieradzan\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ fax: +48 58 523 5128\\
+ e-mail: \href{mailto:adams86@wp.pl}{adams86@wp.pl}\\
+
+ Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ fax: +48 58 523 5124\\
+ e-mail: \href{mailto:adam.liwo@ug.edu.pl}{adam.liwo@ug.edu.pl}\\
\small{
- Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\
+ Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014, updated 12/21/2018\\
}
\end{document}
acid residues in the coarse-grained united residue (UNRES) force field.
{\it J. Chem. Theory Comput.}, {\bf 2014}, 10, 2194-2203.
+\bibitem{sieradzan_2015}
+A.K. Sieradzan, P. Krupa, H.A. Scheraga, A. Liwo, C. Czaplewski.
+Physics-based potentials for the coupling between backbone- and
+side-chain-local conformational states in the united residue
+(UNRES) force field for protein simulations.
+{\it J. Chem. Theory Comput.}, {\bf 2015}, 11, 817-831.
+
+\bibitem{krupa_2017}
+P. Krupa, A. Ha"labis, W. "Rmudzi"nska, S. O"ldziej, H.A. Scheraga, A. Liwo.
+Maximum Likelihood Calibration of the UNRES Force Field for
+Simulation of Protein Structure and Dynamics.
+\textit{J. Chem. Inf. Model}. \textbf{2017}, 57, 2364-2377
+
+\bibitem{karczynska_2018}
+A.S. Karczy"nska, M.A. Mozolewska, P. Krupa, A. Gie"ldo"n, A. Liwo, C. Czaplewski.
+Prediction of protein structure with the coarse-grained UNRES
+force field assisted by small X-ray scattering data and
+knowledge-based information.
+\textit{Proteins: Struct. Func. Bioinfo.}, \textbf{2018}, 86 (S1), 228-239. %DOI: 10.1002/prot.25421.
+
+\bibitem{czaplewski_2018}
+C. Czaplewski, A. Karczy"nska, A.K. Sieradzan, A. Liwo.
+UNRES server for physics-based coarse-grained simulations and prediction
+of protein structure, dynamics and thermodynamics.
+\textit{Nucleic Acids Research}, \textbf{2018}, 46, W304-W309.
+
\end{thebibliography}
\endgroup
\item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
PDB file.
+\item{NSAXS} -- number of distance-distribution bins corresponding to to SAXS
+restraints (to be included in further section of the input).
+
+\item{SCAL\_RAD} -- scaling factor of sidechain radii in calculating Gaussian-smoothed distance distribution.
+
+\item{BOXX, BOXY, BOXZ} - periodic-box dimensions.
+
\end{description}
Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
\end{description}
-\subsubsection{Energy-term weights}
+\subsubsection{Energy-term and restraint weights}
\label{sect:input:main:weights}
(Data list format; subroutine MOLREAD.)
\item{WTOR=number} (real) (1.0d0) --
weight of the torsional term, $U_{tor}$.
+\item{WTORD=number} (real) (1.0d0) --
+weight of the double-torsional term, $U_{tord}$.
+
+\item{WSCCOR=number} (real) (1.0d0) --
+weight of the backbone-sidechain-torsional term, $U_{sccor}$.
+
\item{WANG=number} (real) (1.0d0) --
weight of the virtual-bond angle bending term, $U_b$.
\item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
decreased to zero.
+\item{WSAXS=number} (real) (1.0d0) -- weight of the maximum-likelihood SAXS-restraint term.
+
\end{description}
The defaults are NOT the recommended values. No ``working'' default values
is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
+
+\subsubsection{Distance-distribution (SAXS-restraint) data}
+
+This section contains the probability distribution ($P(r)$) from SAXS
+measurements to be used as restraints through introduction of a maximum-likelihood term.
+Each entry is in a separate like and the number of entries must equal to
+NSAXS specified in the first data record. Each line contains the position
+of the left side of the distance bin and probability-distribution value, for
+example:
+
+\begin{verbatim}
+0.7100E-00 0.2036E-03
+0.1420E+01 0.4221E-03
+\end{verbatim}
+
+The distance-distribution values do not need to be input in normalized form.
+Normalization is carried out automatically. It should be noted that neither
+probabilities nor distances can be zero; otherwise the calculations will crash.
+Therefore, entries with zeros must be eliminated from the data.
+
\subsubsection{Internal coordinates of the initial conformation}
\label{sect:input:main:intcoord}