Month: December 2020

Molecular Modeling

Software

• CHARMM. (Chemistry at HARvard Macromolecular Mechanics). Package of molecular simulation programs, including source code and demos.
• GROMACS. (GROningen MAchine for Chemical Simulations). Free open-source molecular dynamics simulation package.
• Amber. (Assisted Model Building with Energy Refinement). Package of molecular simulation programs, including source code and demos.
• AmberTools. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. It contains NAB (build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models), antechamber and MCPB (create force fields for general organic molecules and metal centers), tleap and sleap (Basic preparation program for Amber simulations), sqm (semiempirical and DFTB quantum chemistry program), pbsa (Performs numerical solutions to Poisson-Boltzmann models), 3D-RISM (Solves integral equation models for solvation), ptraj and cpptraj (structure and dynamics analysis of trajectories), MMPBSA.py and amberlite (Energy-based analyses of MD trajectories)
• OpenMM. High-performance toolkit for CPU/GPU-accelerated molecular dynamics simulation and setup. Can be used as a library or as an application with an intuitive Python interface. Developed, maintained, and provided open-source by Standford University, United States.
• VFFDT. It consists of a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.Proposed by the School of Pharmaceutical Sciences, Wenzhou Medical University
• NAMD. (NAnoscale Molecular Dynamics). Free parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects.
• aMD. (accelerated Molecular Dynamics). an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Distributed by the National Biomedical Computation Resource.
• MATCH. (Multipurpose Atom-Typer for CHARMM). Toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field paramters for molecular mechanics simulation of organic molecules. Developed by the Brooks lab, Michigan university.
• Desmond. Package to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. Developed at D. E. Shaw Research.
• LAMMPS. Program for molecular dynamics. LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors), and coarse-grained or mesoscopic systems.
• MOLARIS-XG. MOLARIS-XG incorporates the methodologies of the former packages ENZYMIX and POLARIS. ENZYMIX is a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method.
• POLARIS is a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach, it is used for the calculation of free energies and electrostactic properties of molecules and macromolecules in solution through the evaluation of the permanent dipoles, induce dipoles, charges, dispersion contributions and hydrophobicity. Provided by the Warshel’s group at the university of Southern California.
• OPENMD. Open source molecular dynamics to simulate liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. sticky atoms, point dipoles, and coarse-grained assemblies).
• ORAC. Free open-source program for Molecular Dynamics simulations. Maintained by the Florence University, Italy.
• AMMP VE. (Another Molecular Mechanics Program). Full-featured molecular mechanics, dynamics, and modelling program that can manipulate both small molecules and macromolecules including proteins, nucleic acids, and other polymers. Uses the VEGA ZZ interface. For MS Windows and Linux. Provided by the Drug Design Laboratory of the University of Milano.
• ACEMD (Accelerating bio-molecular simulations). Production bio-molecular dynamics (MD) software running on graphics processing units (GPUs) on NVIDIA graphics cards. ACEMD reads CHARMM/NAMD and AMBER input files. Distributed by Acellera. Free for 1 year for academic.
• CNS (Crystallography & NMR System). Provides a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
• Adun molecular simulation. Free biomolecular simulator developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF. It is distributed under the GNU General Public License.
• Tinker. Free, complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
• Force Field Explorer. A graphical user interface to the TINKER suite of molecular modeling tools.
• CHARMm. A commercial version of CHARMM with multiple graphical fronts ends.
• MacroModel. Commercial program for molecular modeling. Distributed by Schrodinger.
• MOIL. Public Domain Molecular Modeling Software, including energy calculations, energy minimization, molecular dynamics. Comes with a visualization program (zmoil) for graphic display of individual structures, dynamics, reaction paths and overlay of multiple structures, read PDB CRD DCD and (MOIL specific) PTH formatted files. For Windows, Mac and Linux.
• APBS. Adaptive Poisson-Boltzmann Solver (APBS) is a software for evaluating the electrostatic properties of nanoscale biomolecular systems.
• iAPBS. C/C++/Fortran interface to APBS. This interface enables access to most of APBS capability from within any C/C++ or Fortran code. In addition to the reference implementation, iAPBS/CHARMM, iAPBS/NAMD and iAPBS/Amber modules are also available. These modules extend CHARMM, NAMD and Amber functionality with APBS routines for electrostatic calculations. Provided by the McCammon Group, UCSD.
• Chemsol. Program to calculate solvation energies by using Langevin Dipoles (LD) model of the solvent and ab initio calculations. Also exists as a web service. Provided by the Warshel’s group at the university of Southern California.
• BiKi. The BiKi Life Sciences suite involves several tools (e.g. accelerated binding/unbinding methods) for performing and analyzing MD specifically dedicated to medicinal chemists with the aim of simplifying drug discovery. Provided by BiKi Technologies, Italy.
• Abalone. General purpose molecular modeling program focused on molecular dynamics of biopolymers and molecular graphics. In addition, it can interact with external quantum chemical programs (NWChem, CP2K and PC GAMESS/Firefly. Provided by Agile Molecule.
• Ascalaph. General purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly). Provided by Agile Molecule.
• HyperChem. Provides computational methods including molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods, as well as density functional theory.
• iHyperChem. Limited version of Professional HyperChem. This Level 1 version of iHyperChem allows creating and manipulating molecular systems and explore their structure. It also allows WiFi access to any Professional HyperChem server so that molecules, computations, and results can be transferred between the mobile client (iPhone or iPad) and the server. Provided by HyperChem.
• iHyperChem Free Version. Free Version of iHyperChem for iPad. Provided by HyperChem.
• Spartan. Provides computational methods including molecular mechanics, quantum mechanics, properties calculations (LogP, ovality, etc…), quantification of structural alignment using structure, chemical funtion descriptors or pharmacophore model, etc… Developed by Wavefunction, Inc.
• iSpartan. iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. Molecules are created by two-dimensional sketching and converted into a three-dimensional structure. Low-energy conformations can then be calculated and their geometries be queried. A database of 5,000 molecules (a subset of the Spartan Spectra and Properties Database, SSPD) can furthermore be accessed to obtain NMR and IR spectra, molecular orbitals, electrostatic potential maps, and other atomic and molecular properties. The database can be searched for substructures. Developed by Wavefunction, Inc.
• SCIGRESS. Desktop/server molecular modeling software suite that can apply a wide range of computational models to all types of molecular systems, from small organic molecules, to whole proteins, including linear scaling semiempirical quantum methods for protein optimization and ligand docking. Developed and distributed by Fujitsu, Ltd.
• TopoTools. TopoTools is a VMD plugin for manipulating topology information. It is meant to be a complementary tool to psfgen, which is very much optimized for building topologies for biomolecules. It makes access to the topology related data stored in VMD easily. It also has a number of high-level tools that allow reading and writing of topology file formats that cannot be parsed by the molfile plugins, parsing of parameter and residue database files for generation of complete input files for MD codes like LAMMPS and HOOMD-blue, and replicating or combining multiple systems. Developed by the Temple University, Philadelphia, USA.
• YASARA Dynamics. Adds support for molecular simulations to YASARA View/Model, Using the NOVA, YAMBER or AMBER force fields like AMBER. Provided by YASARA.
• Build model. Tool for creating protein models and their preparation for docking. Refine raw protein structure, add missing sidechains, assign protonation states of side chains at given pH, add missing hydrogen atoms, reconstruct crystallographically-related protein subunits and extract a reference ligand from the structure. Distributed by Moltech. For Windows and linux.
• Pdbfil. Automatically processes the protein coordinate data obtained from PDB for molecular calculations. Adds missing atoms, deletes unnecessary hetero-residues and water molecules, adds and optimizes hydrogen atoms. Atomic attributions like atomic charge or molecular force-field type are also automatically. Distributed by IMMD.
• Protein Preparation Wizard. Tool for correcting common structural problems and creating reliable, all-atom protein models. Distributed by Schrodinger.
• BALL. Biochemical Algorithms Library. Application framework in C++ designed for rapid software prototyping in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization. Free and opensource.
• pDynamo. pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions. Developed by the Institut de Biologie Structurale, Grenoble, France.
• Pcetk. Pcetk (a pDynamo-based continuum electrostatic toolkit) is a Python module extending the pDynamo library with a Poisson-Boltzmann continuum electrostatic model that allows for protonation state calculations in proteins. The module links pDynamo to the external solver of the Poisson-Boltzmann equation, extended-MEAD, which is used for the calculation of electrostatic energy terms. The calculation of protonation states and titration curves is done by using the module’s own analytic or Monte Carlo routines or through an interface to the external sampling program, GMCT. Developed by the Institut de Biologie Structurale, Grenoble, France.
• MMTSB. Multiscale Modeling Tools for Structural Biology. Provides a collection of perl scripts for Structure preparation, Structure analysis, All-Atom Modeling, SICHO Lattice Modeling, Replica Exchange Sampling, Ensemble Computing and Structure Prediction.
• Computer-Aided Drug-Design Platform using PyMOL. PyMOL plugins providing a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE).
• pymacs. Python module for dealing with structure files and trajectory data from the GROMACS molecular dynamics package. It has interfaces to some gromacs functions and uses gromacs routines for command line parsing, reading and writing of structure files (pdb,gro,…) and for reading trajectory data (only xtc at the moment).
• PyRosetta. Interactive Python-based interface to the Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

Web Services

• SwissParam. Provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
• CHARMM-GUI. Provides (optimal, reasonable) CHARMM input files in a GUI fashion so that people can run the input on their machine, Helps people read and modify the input with their purposes, and provides also educational materials such as MM/MD lectures, as well as molecular animations. Provided by the University of Kansas.
• CHARMMing.org. CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results.
• LigParGen. Web-based service that provides OPLS-AA force field parameters for organic molecules or ligands. Beside PGR files, other ouput format includes parameters and topologies to be used with CHARMM, Gromacs, LAMMPS, CNS/X-PLOR, Q, DESMOND, BOSS, OpenMM and MCPRO. Molecules can be input in SMILES, MOL or PDB format with a maximum of 200 atoms. Provided also as a standalone program by the Department of Chemistry, University of Yale, United-States.
• LipidBuilder. A web-server based on a VMD plug-in and CHARMM force field to create, store and share lipid libraries. LipidBuilder automatically generates the topology and template of a given lipid. The lipid topology is created by combining the selected head group, extracted from a built-in library of structures and the provided hydrocarbon chains. Four different classes of hydrocarbons have been parametrized in the CHARMM force field: saturated, unsaturated, branched and cyclopropane. Developed by the EPFL, Lausanne, Switzerland.
• ParamChem. Provides topology and parameters for small organic molecules from CGenFF, for use with CHARMM and GROMACS. Provided by the University of Kentucky.
• PrimaDORAC. A free Web Interface for the Assignment of partial charges, chemical topology, and bonded parameters in small molecules to be used in molecular mechanics or molecular dynamics calculations. Provided by the University of Florence, Italy.
• MATCH server. The MATCH web server allows one to submit a molecule to generate both the topology and parameter file for a given small molecule. Molecule file formats: pdb, sdf, mol, mol2 are all accepted. Provided by the Brooks laboratory, University of Michigan.
• ProteinPrepare. a web application designed to interactively support the preparation of protein structures. Users can upload a PDB file, choose the solvent pH value, and inspect the resulting protonated residues and hydrogen-bonding network within a 3D web interface. Provided by Acellera, Ltd.
• MemBuilder. Prepares the initial configuration of a membrane model composed of different phospholipid molecules. This server is also dedicated to determine the lipid composition of each monolayer to support the asymmetry of the membrane bilayer. Provided by the Tarbiat Modares University.
• CABS-flex. Server for fast simulation of protein structure fluctuations. CABS-flex is a procedure for the simulation of structure flexibility of folded globular proteins. Using an input protein structure the CABS-flex outputs a set of protein models (reflecting the flexibility of the input structure, in all-atom PDB format) ready to use in structure-based studies of protein functions and interactions. Developed by the university of Warsaw.
• Dundee PRODRG2 Server. Converts coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2.
• PDB2PQR Server. Web server to convert PDB files into PQR files and perform an APBS calculation. Protein pKa are calculated using PROPKA.
• PROPKA. Web server to calculate pKa of protein titratable functions.
• PropKa. Web server to calculate pKa of protein titratable functions using PROPKA. Provided by the Drug Design Laboratory of the University of Milano.
• H++. Web server to compute pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment.
• PDB_Hydro. Provides tools for mutating (change side-chains of a PDB file automatically, repair missing side-chains in a PDB file, construct polar hydrogen atoms and assig partial charges for electrostatic calculations) and solvating PDB files.
• POLYVIEW-MM. Web-based platform for animation and analysis of molecular simulations. Enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking.
• CLICK. Web server for superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment. Help establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants or to recognize conformational changes that may have occurred in structural domains or subdomains in one structure with respect to the other.
• SLITHER. Web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters. Predicts whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers.
• AlloDeco. Server that implements a novel model for allostery. It computes the thermodynamic coupling between functional sites in proteins and then determines the contribution of specific interactions to that coupling. First, a 3-dimensional protein structure (PDB file) is transformed into a Gaussian Network Model. The coupled motions of two sites are then decomposed using Canonical Correlation Analysis. Finally, the statistical mechanics-based thermodynamic coupling function formalism is applied to identify interactions that mediate the thermodynamic coupling between the canonical pairs of motions. Developed at Weill Cornell Medical College, New York, United States.
• R.E.D. Server. Web service designed to automatically derive RESP and ESP charges, and to build force field libraries for new molecules/molecular fragments.
• Chemsol web service. Web service for the calculations of solvation free energies using the Langevin Dipoles (LD) solvation model, in which the solvent is approximated by polarizable dipoles fixed on a cubic grid.Also exists as a standalone program. Provided by the Warshel’s group at the university of Southern California.
• MovieMaker. Web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes (simple rotation, morphing between two end conformers, short-scale, picosecond vibrations, ligand docking, protein oligomerization, mid-scale nanosecond (ensemble) motions and protein folding/unfolding). Note: MovieMaker is not a molecular dynamics server and does not perform MD calculations. Provided by the University of Alberta, Canada.
• Superpose. Protein superposition server, using a modified quaternion approach. From a superposition of two or more structures, it generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, Difference Distance Plots, and interactive images of the superimposed structures. Provided by the University of Alberta, Canada.
• ArbAlign. Web implmentation of the Kuhn-Munkres algorithm to optimally align two arbitrarily ordered isomers. Code and web interface provided by the Bucknell University, Lewisburg, USA.

The average price of developing new drug molecules and therefore the time that is taken to publicize them is quite high. The time factor to some extent is being reduced by utilizing modern techniques but the price issue remains a matter of concern.

However, the number of new drugs coming to market has shown only a marginal increase, with respect to the prices. One of the explanations for this trend may be the lack of structural data of the target molecules. Enzymes are the frequent targets of choice because of their involvement in various biochemical pathways in human physiology. Even with enzymes, there can be problems in getting their structural information. Sometimes it is also troublesome to isolate or produce sufficient quantities of the target enzyme to analyze it directly. These obstacles hinder the successful entry of drug candidates into the market. Therefore, there’s an indispensable demand for efficient strategies that could enhance the drug discovery process.

Computational strategies or molecular modelling methods can be utilized to accelerate the drug discovery process for getting new drug molecules. Nowadays there is a trend that multinational pharmaceutical companies and Research Organizations involved in drug discovery have adopted computational methodology at several stages of the design process. Several computational methods complement each other and maybe merged to assist rationalize the drug discovery method. The ultimate challenge in drug styling is to predict and explain the activities of new drug molecules.

Modern drug discovery is a multidisciplinary project, where the role of various computational processes is to utilize experimentally and foretold information in designing new active compounds thereby facilitating and enhancing the speed of discovery of acceptable chemical entities for lead improvement. As far as success stories of drug molecules generated through molecular modeling are concerned, it has been claimed that structure-based drug design strategies have already contributed to the introduction of some drug compounds into clinical trials and for drug approval.

For ligand-based drug design, we have software like quantitative structure-activity relationship (QSAR), Comparative molecular field analysis (CoMFA), Grid independent (GRIND), comparative molecular similarity indices analysis (CoMSIA). For drug discovery, there are methods like Pharmacophore modeling. Similarly, a variety of drug docking programs like AUTODOCK, CDOCKER, DOCK, FlexX, GOLD, GLIDE are available.

No wonder, there is a vast array of jobs in this sector of Molecular Modeling & Drug Designing, owing to its rapid development rate.

Let us have a quick look at the readily available Career options available in Molecular Modeling & Drug Designing field along with eligibility & Salary Details required for each position.

1. Scientist

This is the dream of every Ph. D. scholar that after successful completion of his degree he/she can get involved in research activities as a Scientist. Well established companies like Syngene International Limited, Quantumzyme offer this unique opportunity. Basic requirements include having an experience of 0-8 years, after completing Ph. D. degree. Other than that the employee should understand the process of pharmaceutical discovery and the data and technologies associated. He is also sometimes required to have previous experience in applying molecular modelling methods to structure, ligand, and fragment-based drug discovery projects, ADME modelling and drug ADME profile optimization, a certain degree of proficiency in programming/scripting, working knowledge of databases, etc. All of this can be easily achieved if someone is putting all his efforts in the field of research consistently.

2. Professorship

Another ambition of most of Ph. D. students is to get a Professor title. Numerous universities and institutes which are conducting research in the field of drug designing offer this platform as well. E.g. Rajiv Gandhi Institute of Petroleum Technology, IIT Delhi, RGIPT, offers these positions as Assistant Professors, Professors, or Associate Professors. Along with a Ph. D. degree, the requisite experience is required which fetches them a good amount of income to sustain their living (as per 7th Pay Commission). This is not only a noble profession but also it gives recognition to the Professors and nurtures their hunger to be active research participants. They also get benefits like HRA, TA, etc. Not only this, but professors are also liable to represent their institute at international levels via conferences, symposia, where not only they are honored, they also receive travel grants for pursuing the same.

3. Project Assistant

All those, who are still on the verge of M.Sc. and Ph.D. have another chance to update their resume by adding to their publication record. Regular Project Assistant vacancies are displayed on the university or institutes websites like that of Central Drug Research Institute. These not only fetch them with requisite experience before beginning their Ph.D. journey but also help them financially. Usual pay Scale for a Project Assistant is INR 16000+ HRA p.m. However, not everyone is eligible to be a PA. There is an age limit of 28 yrs to this. Also, their qualifications should be in the Bioinfo and Life science fields with a minimum of 55% marks. Also, depending on the project they may be required to have experience in Computer-Assisted scientific research in Drug Design (CADD) including Bio-molecular modeling, Machine Learning techniques, etc. Familiarity with LINUX based Computer systems also proves to be an advantage.

4.Research Associate

Being a Research Associate in the field of drug discovery in a top company like Glenmark life Sciences Ltd requires you to have experience of 1 – 4 yrs. The candidate is expected to handle targets like the synthesis of APIs following product patent or non-infringing route, literature search for finding suitable reagents and methods for experimentation, other than performing experiments, purification, and concluding the experiments based on analytical results. He is also required to work towards the identification, synthesis, and characterization of impurities/related substances, performing polymorph screening experiments to invent novel solid forms (polymorphs, pseudo-polymorphs, co-crystals, etc). The RA is expected to have good knowledge in data interpretation of NMR, Mass, HPLC, and GC. Preferably data interpretation of PXRD, DSC, TGA, and KF. He is also responsible for documentation of experiments in Lab Note Book (LNB), preparation of reports, and following Good Laboratory Practices (GLP).

5. Bioinformatician in the health sector:

Certain hospitals like The Institute for Trauma Recovery at the University of North Carolina-Chapel Hill, look for Bioinformaticists who are comfortable working with genetic, RNA sequencing, and epigenetic data derived from large human cohort studies. Candidates ought to have expertise in advanced bioinformatics and statistical modelling, artificial intelligence, multilevel modelling, power /factor analyses, and classification analyses targeted around biomarker discovery. Knowledge of SAS, SPSS, R, and/or Python is desired, in conjugation with the flexibility to develop scripts/code as necessary to streamline/optimize analyses. Primary duties of the candidate embody developing analysis plans unitedly with members of the research team, conducting analyses in a timely fashion, deciphering results for the team, and writing analytical strategies for peer-reviewed publications. Candidates are required to have a minimum of a Master’s degree or ideally a Ph.D. degree in Bioinformatics. Qualifications needed for this position include intensive knowledge of applied statistical and computational methods. These jobs facilitate earning approximately 50,000 to 1,00,000 USD per year.

6. Postdoctoral positions

Post Doc Positions are also available throughout the globe, which usually has 2 years duration. However, these are full-time jobs with designated working hours per week. The basic requirements include Ph. D. in structural bioinformatics/ chemoinformatics/ biophysics or a related field with a strong interest in intermolecular interactions alongside a good hold over English. Other specific requirements may include an ability to conduct independent research, 0-5 years experience in molecular modelling and chemoinformatics, experience in at least two topics of structure-based and ligand-based drug design; machine learning methods; MD simulations / enhanced sampling methods, knowledge of programming languages e.g. Python, Perl, Java, SQL, etc. These positions, on one hand, give a lot of exposure and on the other hand, also provide a handsome salary of around 50,000 USD per annum.

7. Research Technician

This is another infamous job profile in the USA, which pays $17 – $25 on an hourly basis. Essential qualifications include a Bachelor’s Degree, MS in biology, or a related field, at least 1-2 years of professional laboratory experience, previous technical experience with basic cellular and molecular biology research techniques and bioinformatics, alongside some basic knowledge of computers. The technician is expected to handle standardized molecular biological, microbiological or biochemical tests and laboratory analyses, CRISPR/Cas9-mediated genome editing experiments, flow cytometry, and cell sorting. He is also responsible for designing and executing advanced experiments and setting strategy. The candidate is also expected to develop, modify, and improve standard operating procedures.

8. Computational Biophysicists:

Certain companies in the USA, as well as India, have other job profiles that need similar skills. Computational biophysicists are one of those. These companies are seeking exceptional computational chemists and biologists, with a track record of extraordinary achievement. Relevant areas of experience might include structural modelling of protein-protein complexes involved in signal transduction or other cellular processes, investigation of conformational changes relevant to the function of protein kinases, direct application of molecular dynamics or other computational methods to drug discovery, ion channels, or other biomolecules, or study of fundamental biophysical problems, such as protein and RNA folding.

9. Teaching in colleges

One can also take up teaching jobs in public institutions if you have a taste in teaching, but before that, you need to be well versed with the techniques and up to date with the latest technologies being used in this field. Also, standard hands-on experience related to molecular modelling and drug designing technique is also desirable.

10. Business Development Executive

It is not so, that drug discovery will lead you to orthodox jobs only. One also gets a chance to handle businesses. Most of the Pharma giants are actively looking for candidates with 2 – 6 yrs experience, who can identify business opportunities from the local and domestic market to expand their pipeline. He should also have marketing skills so as to pursue annual sales in order to achieve quarterly and annual targets/budgeted revenues. These kinds of jobs easily fetch you a handsome salary between INR 3,00,000 – 6,00,000 P.A.  

Foreign universities like the University of Southampton, University of Roehampton, Queen Mary University of London, Kingston University, are regularly hunting for suitable candidates who can join them as Ph. D. scholars in the domain of Computational Biophysics and Bioinformatics. While some of these may be self-funded, others are supported. Here, one gets chances for hands-on training in a wide range of computational methods including bioinformatics and biomolecular simulations. As an international student, one is required to have equivalent degrees in biochemistry, chemistry, physics or a similar discipline and familiarity with molecular modelling and computer programming ability.

Salary Details

As we have already checked, salaries in this field range from Rs. 3 lakh/ year for Research Associate to Rs. 10 lakhs for a managerial post. With experience and increasing responsibility, compensation also grows significantly. They also can receive bonuses throughout the development of a new drug.

The opportunities are abundant. The success rate also depends on several other factors like analytical thinking, desire to learn new methods, leadership, quality management, problem-solving, strong interpersonal skills, strong verbal and written communication, task delegation, sound judgment, and planning and organization skills. What matters most is the capability of the individual to implement the knowledge acquired in a range of fields, his efficiency, and his clean hands.