PROTDES: CHARMM toolbox for computational protein design

We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html

BALL - biochemical algorithms library 1.3

<p>Abstract</p> <p>Background</p> <p>The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.</p> <p>Results</p> <p>Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics.</p> <p>Conclusions</p> <p>BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at <url>http://www.ball-project.org</url>. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.</p

A retrospective analysis of data collected over 05 years for prevalence of Helicobacter pylori infestation in symptomatic patients from Jammu and Kashmir

Introduction: Infection with H. pylori infection is common. About two-third of the population in the world carry H pylori in their bodies. The infection is acquired in the childhood and persist despite of local and systemic immune response.Materials and Methods: This was a prospective observational study done on 1000 patients at a tertiary health care hospital in Jammu, India, over a period of 04 years (March 2016 to March 2020). Written and informed consent regarding the purpose, procedures, and risks was obtained from all patients. Data were collected by conducting personal interview and doing a complete physical examination of the participants of the study. All patients underwent basic investigations as per symptoms and comorbidities. UGIE was performed on all the study participants using a video gastroscope. Gross features of the upper GI tract were noted and biopsies were obtained from the stomach (antrum, body, and fundus), and second part of the duodenum. One antral and one corpus biopsy sample each were used for rapid urease test (RUT).Results: A total of 1000 patients underwent UGIE for different set of complaints. Most common complaint in this study group was epigastric pain (43%) followed by dyspepsia (33.2%) and 80.23% and 78.61% patients were positive for H pylori on RUT. On UGI endoscopy duodenal ulcer was seen in 430 patients and among them 85.34% were H. pylori positive on RUT, gastric ulcer was seen in 240 patients and among them 73.33% were H pylori positive. Most common comorbidity was hypertension in the study group and among these patients 138(88.46%) were H. pylori positive, 2nd common comorbidity was Diabetes mellitus and among them 133(91.86%) were H. pylori positive. Overall prevalence of H. pylori manifestation in study group was seen in 78.5% patients.Conclusion: Among all symptomatic patients enrolled in this study the most symptom was epigastric pain followed by dyspepsia and most common comorbidities in the study group were HTN and Diabetes mellitus. Rapid urease test was performed on UGI endoscopic biopsy specimen for H pylori infestation and 78.5% patients were found to be positive

Physical map of the chromosome 6q22 region containing the oculodentodigital dysplasia locus: analysis of thirteen candidate genes and identification of novel ESTs and DNA polymorphisms

Oculodentodigital dysplasia (ODDD) is an autosomal dominant condition with congenital anomalies of the craniofacial and limb regions and neurodegeneration. Genetic anticipation for the dysmorphic and neurologic features has been inferred in a few families. Our previous linkage studies have refined the ODDD candidate region to chromosome 6q22 --> q23. In an attempt to clone the ODDD gene, we created a yeast artificial chromosome contig with 31 redundant clones spanning the region and identified and ordered candidate genes and markers. Fluorescent in situ hybridization mapped two of these YAC clones to chromosome 6q22.2 telomeric to a known 6q21 fragile site, excluding it as a possible cause of the suggested anticipation. We performed mutation analysis on thirteen candidate genes-GRIK2, HDAC2, COL10A1, PTD013, KPNA5, PIST, ROS1, BRD7, PLN, HSF2, PKIB, FABP7, and HEY2. Although no mutations were found, we identified 44 polymorphisms, including 28 single nucleotide polymorphisms. Direct cDNA selection was performed and fifty-five clones were found to contain sequences that were not previously reported as known genes or ESTs. These clones and polymorphisms will assist in the further characterization of this region and identification of disease genes. Copyright (C) 2002 S. Karger AG, Basel

Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design

<div><p>Noncanonical amino acids (NCAAs) can be used in a variety of protein design contexts. For example, they can be used in place of the canonical amino acids (CAAs) to improve the biophysical properties of peptides that target protein interfaces. We describe the incorporation of 114 NCAAs into the protein-modeling suite Rosetta. We describe our methods for building backbone dependent rotamer libraries and the parameterization and construction of a scoring function that can be used to score NCAA containing peptides and proteins. We validate these additions to Rosetta and our NCAA-rotamer libraries by showing that we can improve the binding of a calpastatin derived peptides to calpain-1 by substituting NCAAs for native amino acids using Rosetta. Rosetta (executables and source), auxiliary scripts and code, and documentation can be found at (<a href="http://www.rosettacommons.org/">http://www.rosettacommons.org/</a>).</p> </div